Digital Commons Network^™

Detection Of Crop Diseases Using Enhanced Variability Imagery Data And Convolutional Neural Networks, Shai Kendler, Ran Aharoni, Sierra N. Young, Hanan Sela, Tamar Kis-Papo, Tzion Fahima, Barak Fishbain

Civil and Environmental Engineering Faculty Publications

The timely detection of crop diseases is critical for securing crop productivity, lowering production costs, and minimizing agrochemical use. This study presents a crop disease identification method that is based on Convolutional Neural Networks (CNN) trained on images taken with consumer-grade cameras. Specifically, this study addresses the early detection of wheat yellow rust, stem rust, powdery mildew, potato late blight, and wild barley net blotch. To facilitate this, pictures were taken in situ without modifying the scene, the background, or controlling the illumination. Each image was then split into several patches, thus retaining the original spatial resolution of the image …

Interplay Between An Atp-Binding Cassette F Protein And The Ribosome From Mycobacterium Tuberculosis, Zhicheng Cui, Xiaojun Li, Joonyoung Shin, Howard Gamper, Ya-Ming Hou, James C Sacchettini, Junjie Zhang

Department of Biochemistry and Molecular Biology Faculty Papers

EttA, energy-dependent translational throttle A, is a ribosomal factor that gates ribosome entry into the translation elongation cycle. A detailed understanding of its mechanism of action is limited due to the lack of high-resolution structures along its ATPase cycle. Here we present the cryo-electron microscopy (cryo-EM) structures of EttA from Mycobacterium tuberculosis (Mtb), referred to as MtbEttA, in complex with the Mtb 70S ribosome initiation complex (70SIC) at the pre-hydrolysis (ADPNP) and transition (ADP-VO4) states, and the crystal structure of MtbEttA alone in the post-hydrolysis (ADP) state. We observe that MtbEttA binds the E-site of the Mtb 70SIC, remodeling the …

Democratizing Bioinformatics Through Easily Accessible Software Platforms For Non-Experts In The Field, Konstantinos Krampis

Publications and Research

No abstract provided.

Early Evidence Of The Sars-Cov-2 B.1.1.529 (Omicron) Variant In Community Wastewater: United States, November–December 2021, Amy Kirby, Rory M. Welsh, Zachary Marsh, Davida S. Smyth, Et Al.

Biology Faculty Publications (Archived)

Notes from the Field: Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater — United States, November–December 2021

Covers: California, Colorado, New York City, Houston

Pparα And Pparγ Activation Is Associated With Pleural Mesothelioma Invasion But Therapeutic Inhibition Is Ineffective, M. Lizeth Orozco Morales, Catherine A. Rinaldi, Emma De Jong, Sally M. Lansley, Joel P. A. Gummer, Bence Olasz, Shabarinath Nambiar, Danika E. Hope, Thomas H. Casey, Y. C. Gary Lee, Connull Leslie, Gareth Nealon, David M. Shackleford, Andrew K. Powell, Marina Grimaldi, Patrick Balaguer, Rachael M. Zemek, Anthony Bosco, Matthew J. Piggott, Alice Vrielink, Richard A. Lake, W. Joost Lesterhuis

Research outputs 2022 to 2026

Mesothelioma is a cancer that typically originates in the pleura of the lungs. It rapidly invades the surrounding tissues, causing pain and shortness of breath. We compared cell lines injected either subcutaneously or intrapleurally and found that only the latter resulted in invasive and rapid growth. Pleural tumors displayed a transcriptional signature consistent with increased activity of nuclear receptors PPARα and PPARγ and with an increased abundance of endogenous PPAR-activating ligands. We found that chemical probe GW6471 is a potent, dual PPARα/γ antagonist with anti-invasive and anti-proliferative activity in vitro. However, administration of GW6471 at doses that provided sustained plasma …

Editorial: Adaptation Of Trees To Climate Change: Mechanisms Behind Physiological And Ecological Resilience And Vulnerability, Andrea Ghirardo, James D. Blande, Nadine K. Ruehr, Raffaella Balestrini, Carsten Külheim

Michigan Tech Publications, Part 1

No abstract provided.

Loss Of Irf2bpl Impairs Neuronal Maintenance Through Excess Wnt Signaling, Paul C Marcogliese, Debdeep Dutta, Shrestha Sinha Ray, Nghi D P Dang, Zhongyuan Zuo, Yuchun Wang, Di Lu, Fatima Fazal, Thomas A Ravenscroft, Hyunglok Chung, Oguz Kanca, Jijun Wan, Emilie D Douine, Undiagnosed Diseases Network, Loren D M Pena, Shinya Yamamoto, Stanley F Nelson, Matthew Might, Kathrin C Meyer, Nan Cher Yeo, Hugo J Bellen

Duncan NRI Faculty and Staff Publications

De novo truncations in Interferon Regulatory Factor 2 Binding Protein Like (IRF2BPL) lead to severe childhood-onset neurodegenerative disorders. To determine how loss of IRF2BPL causes neural dysfunction, we examined its function in Drosophila and zebrafish. Overexpression of either IRF2BPL or Pits, the Drosophila ortholog, represses Wnt transcription in flies. In contrast, neuronal depletion of Pits leads to increased wingless (wg) levels in the brain and is associated with axonal loss, whereas inhibition of Wg signaling is neuroprotective. Moreover, increased neuronal expression of wg in flies is sufficient to cause age-dependent axonal loss, similar to reduction …

An Estrogen-Sensitive Hypothalamus-Midbrain Neural Circuit Controls Thermogenesis And Physical Activity, Hui Ye, Bing Feng, Chunmei Wang, Kenji Saito, Yongjie Yang, Lucas Ibrahimi, Sarah Schaul, Nirali Patel, Leslie Saenz, Pei Luo, Penghua Lai, Valeria Torres, Maya Kota, Devin Dixit, Xing Cai, Na Qu, Ilirjana Hyseni, Kaifan Yu, Yuwei Jiang, Qingchun Tong, Zheng Sun, Benjamin R Arenkiel, Yanlin He, Pingwen Xu, Yong Xu

Faculty, Staff and Students Publications

Estrogen receptor–α (ERα) expressed by neurons in the ventrolateral subdivision of the ventromedial hypothalamic nucleus (ERαvlVMH) regulates body weight in females, but the downstream neural circuits mediating this biology remain largely unknown. Here we identified a neural circuit mediating the metabolic effects of ERαvlVMH neurons. We found that selective activation of ERαvlVMH neurons stimulated brown adipose tissue (BAT) thermogenesis, physical activity, and core temperature and that ERαvlVMH neurons provide monosynaptic glutamatergic inputs to 5-hydroxytryptamine (5-HT) neurons in the dorsal raphe nucleus (DRN). Notably, the ERαvlVMH → DRN circuit responds to changes in ambient temperature and nutritional states. We further showed …

Grandi Byen-Supporting Child Growth And Development Through Integrated, Responsive Parenting, Nutrition And Hygiene: Study Protocol For A Randomized Controlled Trial, Patricia L Kohl, Emmanuel A Gyimah, Jenna Diaz, F Matthew Kuhlmann, Sherlie Jean-Louis Dulience, Fithi Embaye, Derek S Brown, Shenyang Guo, Joan L Luby, Jennifer L Nicholas, Jay Turner, Melissa Chapnick, Joseline Marhone Pierre, Jacques Boncy, Rony St Fleur, Maureen M Black, Lora L Iannotti

2020-Current year OA Pubs

BACKGROUND: Poor child growth and development outcomes stem from complex relationships encompassing biological, behavioral, social, and environmental conditions. However, there is a dearth of research on integrated approaches targeting these interwoven factors. The Grandi Byen study seeks to fill this research gap through a three-arm longitudinal randomized controlled trial which will evaluate the impact of an integrated nutrition, responsive parenting, and WASH (water, sanitation and hygiene) intervention on holistic child growth and development.

METHODS: We will recruit 600 mother-infant dyads living in Cap-Haitien, Haiti and randomize them equally into one of the following groups: 1) standard well-baby care; 2) nutritional …

Effect Of Seeding Rates On Productivity And Quality Of Alfalfa In Northern Area Of Korea, Jong Geun Kim, C. Liu, S. N. Wei, Y. F. Li, E. C. Jeong, H. J. Kim

IGC Proceedings (1977-2023)

Alfalfa cultivation in South Korea is not common. There are many reasons, but low productivity has been extremely limited. Although alfalfa growth was poor due to boron deficiency in the soil, the problem has recently been solved. Nevertheless, the cultivation of alfalfa is not expanding. About 200,000 tonnes of alfalfa hay are imported every year. Therefore, this study was conducted to find a way to replace imported hay by expanding alfalfa cultivation in Korea. Alfalfa (P5444) was sown in northern part of South Korea (Pyeongchang). Alfalfa was sown in September 2018 with different seeding rates (20, 30 and 40 kg/ha) …

Effect Of Prompt-Delayed Packaging And Ensiling Time On Fermentation And Aerobic Stability Of Soybean Curd Residue, Ajmal Wali, Takeshi Tsuruta, Naoki Nishino

IGC Proceedings (1977-2023)

Wet soybean curd residue (SCR) obtained from two tofu factories (F1 and F2) was anaerobically stored with or without added beet pulp (BP). Sealing was performed on the day of tofu production (prompt sealing [PS]) or 2 days after SCR was piled and unprocessed (delayed sealing [DS]). Predominant lactic acid fermentation was observed regardless of the sealing time and BP addition. Acinetobacter spp. were the most abundant (> 67%) bacteria in pre-ensiled SCR, regardless of the factory and sealing time. In PS silage, the abundances of typical lactic acid-producing bacteria, such as Lactobacillus, Pediococcus, and Streptococcus spp. reached …

Effect Of Native Grassland Intensification Over Cattle Performance, N. Caram, F. Casalás, M. Cadenazzi, R. Zanoniani, P. Boggiano

IGC Proceedings (1977-2023)

The objective was to evaluate the effect of different levels of intensification in native grassland over cattle live weight gain (LWG), stocking rate (SR) and average daily gain (ADG) in Uruguay. The study was carried out in 7.8 ha in Paysandú, between winter 2015 and autumn 2019. Experiment was a randomized complete block design, with 4 replicates. The four treatments applied were native grassland (NG), NG overseeded with Trifolium pratense (6 kg.ha^-1) and Lotus tenuis (6 kg.ha^-1) + 40 kg.ha^-1 of P₂O₅ (NGO), NG fertilized with 60 kg.ha^-1 of N + …

Relationship Between Exchangeable Acidity And Persistence Of Orchardgrass (Dactylis Glomerata) In Temperate Pastures Under Different Management, H. Kakihara, S. Ogura

IGC Proceedings (1977-2023)

Orchardgrass is a high productive, highly nutritive grass, but its persistence is low under acid soil condition. Therefore, to obtain the information on the effect of soil acidity on the persistence of orchardgrass in acid soil grasslands, we investigated the relationship between exchangeable acidity (y₁) and orchardgrass in sown pastures. Eight temperate pastures (four cutting meadows [CMs] and four cattle grazing pastures [GPs]) were used for vegetation survey and soil samplings. Six or three line transects (50 m each) were fixed in each meadow or pasture, and measurement location (three quadrats 20 cm×20 cm in size and 50 …

Productivity Of Grasslands In Wielkopolska In Conditions Of Weather Variables Changes In The Last 34 Years, B. Golińska, M. Czerwiński, P. Goliński

IGC Proceedings (1977-2023)

The purpose of this study was the assessment of the effect of climatic changes since 1985 on the productivity of grasslands in Wielkopolska region (Poland). The weather data (precipitation sum, mean, maximum and minimum air temperature, insolation, relative air humidity and wind speed) were collected from 1985 to 2018 at five weather stations located in the region that belong to the Institute of Meteorology and Water Management. Using this data, trends of Standardized Precipitation Evapotranspiration Index (SPEI) were determined. Grassland productivity was estimated from data collected by the Central Statistical Office, that refer to meadow hay production for each commune …

The Diversity Of Poisonous Plant Patches In The Arid Rangelands Of Namaqualand, South Africa, T. Jamalie, M. I. Samuels, C. F. Cupido, F. L. Müller, W. L. Engelbrecht, T. Dube, R. S. Knight

IGC Proceedings (1977-2023)

The Namaqualand region in South Africa is part of the richest arid biodiversity hotspot in the world. Plant distribution and diversity here are impacted by various biophysical and anthropogenic factors. In these landscapes, poisonous plant patches, which pose serious threats to livestock, are widespread but their contribution to the regions biodiversity are not fully understood. This study assessed their plant diversity and compared its matrix. This study was conducted in the semi-arid to arid Steinkopf pastoral area located in Namaqualand where livestock is still herded daily. Twenty-five paired sites were selected based on the dominance of poisonous plants within the …

Isotopic Δ15N Signature Of Grass-Alone And Grass-Legume Tropical Pastures To Estimate Sources Of Nitrogen To Grasses In Farmer Managed Pastures, Daniel M. Villegas, J. Velasquez, J. Arango, K. Obregon, Idupulapati M. Rao, G. Rosas, A. Oberson

IGC Proceedings (1977-2023)

Vast areas of tropical forest have been converted into pastures sown with introduced grasses (Urochloa spp.). The majority of pastures exist in some stage of degradation, which has dramatic ecological and economic consequences. Our objective was to determine isotopic ¹⁵N signature of grass alone and grass-legume pastures to estimate sources of nitrogen (N) to grasses in farmer managed pastures. This work contributes to enhancing the sustainability of tropical pastures in forest margins through the integration of legumes. The overarching hypothesis tested was that legumes associated with grasses will improve nutrient supply via symbiotic fixation and mobilization of soil …

Landscape-Level Impacts Of Mesquite Canopy Cover On Herbaceous Species Composition, D. B. Murray, C. E. Cooper

IGC Proceedings (1977-2023)

Woody encroachment of mesquite (Prosopis) and acacia (Acacia) species into grasslands has widespread and ongoing impacts on grassland ecosystems. Changes in the herbaceous layer are associated with changes in the canopy cover of these sparse-canopied species, which do not exclude the herbaceous component, but often change species composition under the canopy relative to surrounding open areas. These effects are often differential based on productivity of the site and herbaceous species composition of the grassland. Here we investigated landscape-scale changes in the herbaceous composition resulting from changes in canopy cover of honey mesquite (Prosopis glandulosa) …

Interactive Effects Of Drought And Fire On Co-Existing Woody And Herbaceous Communities In A Temperate Mesic Grassland, R. Keen, J. Nippert, E. Tooley, K. O’Keefe, S. Bachle, M. Sandwick

IGC Proceedings (1977-2023)

Increased drought and woody encroachment are likely to have substantial and interactive effects on grassland carbon and water cycling in the future. However, we currently lack necessary information to accurately predict grassland responses to drought-by-fire interactions in areas experiencing woody encroachment. A more thorough understanding of these interactive effects on grass-shrub physiology would improve the effectiveness of demographic vegetation models and refine predictions of future changes in grassland ecosystem function. To this end, we constructed passive rainout shelters over mature Cornus drummondii shrubs and co-existing grasses in two fire treatments (1-year and 4-year burn frequency) at the Konza Prairie Biological …

Interacting Effects Of Disease And Weather Variability On Rangeland Biodiversity Associated With Black-Tailed Prairie Dog (Cynomys Ludovicianus) Colonies, Courtney J. Duchardt, J. D. Hennig, D. Pellatz

IGC Proceedings (1977-2023)

Rangeland ecosystems worldwide are experiencing novel pressures during the Anthropocene, including land conversion, disease dynamics, non-native species, and climate change. These issues can be compounded in rangelands occupied by burrowing rodents. Often considered keystone species important for maintaining rangeland biodiversity, these species often experience widespread control efforts because of their potential to reduce forage for livestock. We examined the effects of climatic variation and disease on bird communities associated with a North American burrowing rodent, the black-tailed prairie dog (Cynomys ludovicianus). Following an outbreak of sylvatic plague (Yersinia pestis) in the prairie dog population, we observed …

Influence Of Grazing Intensity On Nutrient Concentrations In Grass Tissue: Evidence From Two Savannah Grass Species, C. Munyati

IGC Proceedings (1977-2023)

High grazing intensity can accelerate the recycling of animal nutrients on savannah rangelands through the deposition of dung and, subsequently, nutrient mineralisation, uptake and concentration in grass tissue. The actual magnitude of this influence can vary depending on the grazing system. This study derived grazing system-dependent magnitudes of the influence of grazing intensity on concentrations of major (N, P, K, Ca, Mg, Na) and trace (B, Co, Cu, Cr, Fe, Mn, Mo, Ni, Se, Zn) animal nutrients in above ground grass tissue. Two grass species were examined: Brachiaria nigropedata, a decreaser, and Eragrostis lehmanniana, an increaser. For the …

Medical School Watercooler Newsletter - January 20, 2022, Lindsey Lyle

Watercooler Newsletter

This is the January 20, 2022 edition of the Frederick P. Whiddon College of Medicine's newsletter - Watercooler.

Contents include:

• Pediatrics faculty to present on COVID variant at virtual town hall
• Research, educate, advocate: Nelson fights back against Alzheimer’s disease
• Herrera presents at international nephropathology forum
• Meet a Med Student: Jack Galla
• OB-GYN Interest Group hosts women’s health drive

Proteomic Analysis Of Epididymal And Ejaculated Sperm And Respective Fluids, Saulo Menegatti Zoca, Emmalee J. Northrop-Albrecht, Julie Walker, Robert A. Cushman, George Perry

SDSU Beef Day 2022 Summary Publication

Study Description:

Ejaculated and epididymal semen was collected from mature Angus bulls (n = 9), and then centrifuged to separate sperm and fluid. Fluids were collected and sperm pellets were resuspended in a high ionic solution and vortexed to remove loosely attached proteins. Sperm samples were centrifuged, and the supernatant was collected. Samples collected for protein analysis were snap frozen in liquid nitrogen and stored at -80 ºC. Protein analysis was performed by liquid chromatography with tandem mass spectrometry (LCMS/MS). Yearling Angus cross bulls (n = 40) were used for sperm cultures. Ejaculated (n = 20) and epididymal (n = …

Residue–Residue Contact Changes During Functional Processes Define Allosteric Communication Pathways, Xin-Qiu Joe Yao, Donald Hamelberg

Chemistry Faculty Publications

Allosteric regulation plays a central role in orchestrating diverse cellular processes. A prerequisite for allostery is a flexible biomolecule within which two distal sites can communicate via concerted or sequential conformational changes. We introduce a computational method to elucidate allosteric communication pathways, comprising critical allosteric residues, in biomolecules by taking advantage of conformational changes during a functional process. Conformational changes are modeled explicitly since they modulate the network of residue–residue interactions, which could propagate allosteric signals between two or more distal sites. The method implements the suboptimal path analysis in the framework of the difference contact network analysis or dCNA. …

The Ancient And Evolved Mouse Sperm-Associated Antigen 6 Genes Have Different Biologic Functions In Vivo, Yi Tian Yap, Wei Li, Qi Zhou, Sarah Haj-Diab, Dipanwita Dutta Chowdhury, Asmita Vaishnav, Pamela Harding, David C. Williams, Brian F. Edwards, Jerome F. Strauss, Zhibing Zhang

Hypertension and Vascular Research Articles

Sperm-associated antigen 6 (SPAG6) is the mammalian orthologue of Chlamydomonas PF16, an axonemal central pair protein involved in flagellar motility. In mice, two Spag6 genes have been identified. The ancestral gene, on mouse chromosome 2, is named Spag6. A related gene originally called Spag6, localized on mouse chromosome 16, evolved from the ancient Spag6 gene. It has been renamed Spag6-like (Spag6l). Spag6 encodes a 1.6 kb transcript consisting of 11 exons, while Spag6l encodes a 2.4 kb transcript which contains an additional non-coding exon in the 3′-end as well as the 11 exons found in Spag6. The two Spag6 genes …

Usa V. Janell Robinson

2022 Decisions

USDC for the District of New Jersey

A Biological Condition Gradient For Caribbean Coral Reefs: Part Ii. Numeric Rules Using Sessile Benthic Organisms, Deborah L. Santavy, Susan K. Jackson, Benjamin Jessup, Christina Horstmann, Caroline Rogers, Ernesto Weil, Alina Szmant, David Cuevas Miranda, Brian K. Walker, Christopher Jeffrey, David Ballantine, William S. Fisher, Randy Clark, Hector Ruiz Torres, Brandi Todd, Sandy Raimondo

Marine & Environmental Sciences Faculty Articles

The Biological Condition Gradient (BCG) is a conceptual model used to describe incremental changes in bio- logical condition along a gradient of increasing anthropogenic stress. As coral reefs collapse globally, scientists and managers are focused on how to sustain the crucial structure and functions, and the benefits that healthy coral reef ecosystems provide for many economies and societies. We developed a numeric (quantitative) BGC model for the coral reefs of Puerto Rico and the US Virgin Islands to transparently facilitate ecologically meaningful management decisions regarding these fragile resources. Here, reef conditions range from natural, undisturbed conditions to severely altered or …

The Weekly Challenger, January 20, 2022, The Weekly Challenger, Et Al

Weekly Challenger Newspaper Collection

The January 20, 2022, issue of The Weekly Challenger.

2022 January 20-22, Faculty Senate Minutes, State University Of New York At Cortland

Minutes

Faculty Senate Minutes, January 20-22, 2022

Advancement of Historically Underrepresented Faculty

2022 January 20, Faculty Senate Minutes, State University Of New York At Cortland

Minutes

Faculty Senate Minutes, January 20 2022

Self-Conscious Emotions And The Right Fronto-Temporal And Right Temporal Parietal Junction, Adriana Lavarco, Nathira Ahmad, Qiana Archer, Matthew Pardillo, Ray Nunez Castaneda, Anthony Minervini, Julian Keenan

Department of Biology Faculty Scholarship and Creative Works

For more than two decades, research focusing on both clinical and non-clinical populations has suggested a key role for specific regions in the regulation of self-conscious emotions. It is speculated that both the expression and the interpretation of self-conscious emotions are critical in humans for action planning and response, communication, learning, parenting, and most social encounters. Empathy, Guilt, Jealousy, Shame, and Pride are all categorized as self-conscious emotions, all of which are crucial components to one’s sense of self. There has been an abundance of evidence pointing to the right Fronto-Temporal involvement in the integration of cognitive processes underlying the …