bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted RNA Sequencing of FFPE Prostate Biopsies and Matched Prostatectomies
Authors: Sharma Nitya V. , Pellegrini Kathryn L. , Osunkoya Adeboye O. , Gillespie Theresa , Petros John , Huang Eugene , Sanda Martin G. , Moreno Carlos S. 
Published: November 2023

One of the significant challenges with management of prostate cancer is discriminating between aggressive and indolent disease at the time of diagnosis, in order to make clinical decisions on the optimal course of therapy. While biopsies are critical for definitive diagnosis of prostate cancer, it is not known whether RNA biomarker signatures that have been developed using prostatectomy tissues are adequately represented by biopsy specimens. Additionally, the fact that prostate cancers are subject to significant clonal heterogeneity adds to the challenge of applying prognostic signatures to biopsy‐derived RNA. To interrogate whether it is feasible to use prognostic RNA signatures with biopsy tissues, we employed targeted RNA‐Seq on 24 matched biopsy‐radical prostatectomy (RP) pairs and 70 unmatched biopsies. We optimized the Agilent Sure Select Targeted RNA‐Seq protocol to enable targeted RNA‐seq of FFPE RNA, and generated 135 sequencing libraries. Our targeted sequencing panel included 295 genes derived from multiple published prognostic RNA signatures, including our own published 24 gene signature (Sig24), which is prognostic of biochemical recurrence following radical prostatectomy. We identified a subset of 9 out of 295 genes, 1 of which belonged to the Sig24 signature, that were consistently expressed among biopsies and exhibit a relatively high correlation in matched RPs. We also found insignificant gene expression variation among multiple biopsies within the same patient. We calculated Sig24 scores for each matched biopsy‐radical prostatectomy pair, and found that only 8 out of 24 patients had biopsy‐RP pairs with consistent grouping, suggesting that non‐targeted biopsies may not reliably reflect the gene patterns expressed in corresponding primary tumors. Taken together, these data support the use of targeted biopsies and demonstrate the feasibility of targeted RNA‐seq of FFPE biopsy samples.Support or Funding InformationAtlanta Clinical and Translational Science Institute (ACTSI) NIH UL1TR000454‐06 ACTSI, NIH U01CA113913‐suppl, Winship Prostate Pilot Award, NIH Cancer Center Support Grant P30CA138292.
Investigating Methylated Arginine Residues in PGC‐1α
Authors: Cuala Janielle Miguel , Osuji Immaculeta Miguel , Zurita‐Lopez Cecilia 
Published: November 2023

Peroxisome proliferator‐activated receptor γ coactivator 1α (PGC‐1α) participates in the regulation of both carbohydrate and lipid metabolism and is activated by insulin. For these reasons, it has been implicated in obesity and diabetes. PGC‐1α is subjected to many post‐translational modifications including phosphorylation of Ser570 by protein kinase B (Akt/PKB), which stops gluconeogenesis and fatty acid oxidation. In addition, PGC‐1α is methylated by protein arginine methyltransferase 1 (PRMT1) at several arginine residues, including Arg665, Arg667 and Arg669 which enhance its regulation. Evidence for additional arginine methylated sites have been found, but the exact sites remain unknown. We set out to identify methylated arginine residues on PGC‐1α. PRMT1 and truncated constructs corresponding to PGC‐1α were expressed and purified. Next, in vitro methylation reactions were carried out, followed by detection of methylated arginine residues by various methods including immunoblot and autoradiography. Identification of the methylated arginine residue(s), will enhance our understanding of PGC‐1α with the broader goal of determining its regulation in the context of obesity and diabetes.Support or Funding InformationMinority Biomedical Research Support‐Research Initiative for Scientific Enhancement (MBRS‐RISE) Fellowship. Grant: R25 GM061331
Variation in Food Group Availability and Nutrient Composition Across Food Pantry Inventories
Authors: Andersen Catherine J. , Ragonesi Nicholas , Cintron‐Rivera Layra , Murray Kristina , Cerrito Brianna , Melville Jamie , Dupree Lydia , McCabe Michelle 
Published: November 2023

Food insecurity has been linked to an increased risk of nutrition‐related health disparities and dependency on emergency food assistance programs, including food pantries. Given the diverse nature by which food pantries operate and acquire food inventory, we aimed to investigate variations in food group availability and overall nutrient composition of inventories at three food pantries in different districts of Bridgeport, Connecticut (Pantry 1, zip code 06604; Pantry 2: zip code 06605; and Pantry 3: zip code 06606). Foods were categorized as grains (refined or whole), vegetables (dark‐green leafy, red & orange, legumes, starchy, or other), fruits, protein, dairy, or oils, as defined by the Dietary Guidelines for Americans 2015–2020. Nutrient composition of food items was further analyzed to determine total and saturated fat, cholesterol, sodium, total sugar, and fiber content of pantry inventories. We observed that Pantry 1 had the largest variety of food items (n = 115 different products), as compared to Pantries 2 (n = 40) and 3 (n = 35). Grains were found to be the most predominant food type at all pantries, representing 38.3%, 57.5%, and 45.7% of all products in Pantries 1, 2, and 3, respectively. Of all grain products, refined grain foods were most abundant at Pantries 1 (70.5%), 2 (78.3%), and 3 (87.5%), as compared to whole grain products (29.6%, 21.7%, and 12.5%). Aside from oil products, which were not present at any pantries, fruit (10.4%, 5%, and 2.9%) and dairy (1.7%, 5%, and 11.4%) products represented the smallest proportion of food items, albeit to varying degrees. Variation in the prevalence of vegetable type was additionally observed across pantries, with Pantry 1 supplying an assortment of legumes (14.3%), and dark‐green leafy (2.4%), red & orange (42.9%), starchy (16.7%), and other (23.8%) vegetables. In contrast, Pantry 2 only supplied dark‐green leafy (40.0%), red & orange (10.0%), starchy (10.0%), and other (40%) vegetables, whereas Pantry 3 inventory lacked dark‐leafy vegetables and legumes. In comparing nutrient compositions of all inventory foods across pantries, we observed that Pantry 1 food items contained significantly lower amounts of total and saturated fat, total sugar, cholesterol, and increased fiber per average serving when compared to the inventory foods of Pantry 3. Together, these findings suggest that food selection and nutritional quality varies significantly across food pantries within a single city.Support or Funding InformationFairfield University College of Arts and Sciences
Accessibility and Availability of Food Store in Urban Area of Korea
Authors: Jang Mi Jin , Kim Seong‐Ah , Chung Sangwon , Joung Hyojee 
Published: November 2023

Food stores are known to play an important role in food choice of people and thus may also be critical determinants for their nutrition and health status. The aim of this research was to assess accessibility and availability of food store in a city. A total of 73 food stores, including 13 chain supermarkets, 17 non‐chain supermarkets, 17 convenience stores, 9 marketplaces (including farmer's market, street market from truck), and 17 specialty stores (butcher's, organic or produce shop) were recruited from the list of telephone directory and search engine between 2013 and 2014 in urban area of Hwaseong‐si, Korea. A structured questionnaire previously developed was applied to collect information on general characteristics and accessibility of food store and availability of selling products. The store size of chain supermarket was predominantly bigger than other food stores (p<0.01), and the majority of the customers in food store were female except non‐chain supermarket and convenience store. The age group of major customers were 30–40' in supermarkets, 40–50's in marketplace and specialty store, and 20–30's in convenience store.. The ‘best‐selling product’ in the chain supermarket were unprocessed food such as vegetables, fruits, meats and milk, but ‘ready‐to‐eat products’ like beverages, milk, snack and noodles were highly ranked in other type of food stores. All food stores showed high accessibility to parking lot (82~100%) as well as to public transportation (78~100%), but chain supermarket and specialty store had the easiest accessibility with home delivery as well as convenient order system by phone and internet. Healthy food options such as whole or mixed grain, low/no sodium, low fat, low calorie products were widely available in the chain supermarket, while was mostly limited in convenience stores. However, over half of convenience stores were available for low fat milk, low calorie noodle and soda. Chain supermarket offers the greatest variety in vegetables and fruits, but convenience store, marketplace and specialty store do considerably lower diversity of produce (p<0.001). This study showed that accessibility and availability of food stores are different from store type in urban area. Further researches to evaluate food stores in other areas are required to develop food environment intervention programs.Support or Funding InformationThis work was supported by the ‘Development of Agriculture Science Technology’ projected from the Rural Development Administration (PJ008995).
Transmission Electron Microscopy Analysis of Visceral and Subcutaneous Lymph Nodes: High Fat Diet‐Induced Morphological Changes
Authors: Foster Michelle , Vanderpool Kimberly 
Published: November 2023

Inflammation, induced by excessive adipose tissue accumulation, appears to link obesity to disease risk yet little attention has been devoted to the lymphoid tissues embedded within adipose tissue. These structures are the primary site for the development of protective immunity, including antibody and cellular immune responses. Hence, any disease process that affects lymphoid tissues will also directly impact immunity, including responses to pathogens, infections, cancer and vaccines. We examined how obesity alters secondary lymphatic tissue structure and immune cells encapsulated within. 4 month C57BL/6 male mice were fed standard rodent Chow (n = 3) (Harlan – 7002: 18% of calories from fat and 49% from carbohydrates) or Western high fat diet (n = 3) (HFD, Harlan ‐ TD.88137: 42% of calories primarily from saturated fat from milkfat and 42% from sucrose) for 6 months. Body mass was recorded for the duration of the study. Because visceral, but not subcutaneous, adipose tissue accumulation is highly associated with metabolic disease, visceral and subcutaneous lymph nodes were analyzed via transmission electron microscopy. HFD‐induced obesity caused numerous morphology changes to immune cells and sinus space in both visceral and subcutaneous lymph nodes. Lymph nodes of HFD mice contained large amounts of cellular debris indicative of damaged or dead cells. Large engulfing macrophages where associated with debris dense regions. HFD intake also increased collagen and microfibrils within lymph nodes. These structural proteins are products of dysregulated enlarged fibroblastic reticular cells (FRCs). Under normal conditions, FRC network maintains T cell homeostasis and cellular interactions needed for a proper immune response. Disruption of this network was associated with increased sinus spacing between immune cells. Overall, HFD‐induced obesity caused cellular death and macrophage activation. We postulate obesity associated inflammation causes FRCs to‐induce fibrosis within lymph nodes and likely contributes to increased sinus spacing and subsequently reduced immune cell interactions. The consequential outcomes on immune regulation would likely contribute to the immunosuppression and lymphatic vessel dysfunction demonstrated to occur during obesity.Support or Funding InformationNIH R03DK099425
Thanks For The Memories: Cocaine Cue Reactivity and the 5‐HT2A receptor (5‐HT2AR) System
Authors: Holliday Erica , Sholler Dennis J , Fox Robert G , Stutz Sonja J , Dineley Kelly T , Anastasio Noelle C , Cunningham Kathryn A. 
Published: November 2023

Success in recovery from cocaine use disorder (CUD) is challenged by vulnerability to relapse, propelled in part by exposure to cocaine‐linked cues (‘cue reactivity’; Anastasio et al., Neuropharmacol 76 Pt B:460, 2014). The memory for the association between environmental cues (e.g., drug paraphernalia, people, places) and cocaine‐taking engages the serotonin (5‐HT) 5‐HT2A receptor (5‐HT2AR) system in the medial prefrontal cortex (mPFC) (Penkowski et al., Psychopharmacol 213:307, 2011), a region importantly involved in associative learning processes (Harvey, Learn Mem 10:355, 2003). In the present experiment, we hypothesized that an engineered loss of the 5‐HT2AR in the mPFC would alter cocaine cue reactivity as well as cued fear learning. A short hairpin RNA (shRNA) that efficiently knocks down over 90% of 5‐HT2AR mRNA in vitro was designed, validated, and packaged into an adeno‐associated viral (AAV) vector; the non‐silencing control (NSC) hairpin had no effect on 5‐HT2AR mRNA expression. Rats acquired cocaine self‐administration (0.75 mg/kg/inf) to stability prior to bilateral microinfusion of 5‐HT2AR‐shRNA‐eGFP AAV or NSC‐eGFP‐AAV into the mPFC (AP: +3.0 mm; ML: +1.4 mm; DV: −5.1, −4.1, −3.1 mm; relative to Bregma) (n=10–12/group). One month after microinfusions, rats were returned to the chambers and cue reactivity was assessed as lever presses for drug‐associated cues. In a second cohort, microinfusion of 5‐HT2AR‐shRNA‐eGFP AAV or NSC‐eGFP‐AAV into the mPFC occurred one month prior to the acquisition of trace fear conditioning (n=5–7/group). Acquisition consisted of two presentations of a conditioned stimulus (white noise; 85dB) and a 500 ms trace interval before presentation of the unconditioned stimulus (foot shock; 0.75 mA). Freezing in the context or upon presentation of the auditory cue served as measures of hippocampal and mPFC involvement, respectively. Western blot analysis indicated that 5‐HT2AR protein expression was significantly reduced following 5‐HT2AR shRNA vs. NSC (p<0.05). The knockdown of the 5‐HT2AR in the mPFC significantly augmented cue reactivity (p<0.05 vs. NSC) and increased freezing upon exposure to the auditory cue (p<0.05 vs. NSC), with no difference in acquisition or freezing to the context. These data suggest that loss of tone in the 5‐HT2AR system in the mPFC results in dysregulation of cue‐associated behavior in two distinct paradigms of associative learning. Future studies will explore the molecular mechanisms through which decrements in 5‐HT2AR mPFC signaling affect cue‐mediated behavior.Support or Funding InformationT32DA07287 (EDH, DJS), P50DA033935 (KAC/NCA), K05DA020087 (KAC)
Behavioral and Pharmacokinetic Properties of the Putatively‐Inert DREADD Ligand Clozapine‐N‐Oxide (CNO) in Rats and Mice
Authors: Porter Joseph H. , Manvich Daniel F. , Webster Kevin A. , Foster Stephanie L. , Farrell Martilias S. , Weinshenker David 
Published: November 2023

Clozapine‐N‐oxide (CNO) is a major metabolite of the antipsychotic drug clozapine that has been utilized in many studies as an “inert” molecule to activate DREADDs (Designer Receptors Exclusively Activated by Designer Drugs). Recently, MacLaren et al (2016) demonstrated thatCNO produced reduced acoustic startle reflex and significantly attenuated d‐amphetamine‐induced hyperlocomotion in rats that lacked DREADD receptor expression. The present study examined the discriminative stimulus properties of CNO in both mice and rats trained to discriminate 1.25 mg/kg clozapine from vehicle in a two‐lever drug discrimination paradigm. After clozapine discrimination was established, substitution tests with CNO (1.0 – 40.0 mg/kg) revealed that CNO partially substituted for the clozapine stimulus in both species. Furthermore, pharmacokinetic studies using plasma samples from separate groups of rats and mice revealed that doses of CNO, which produced partial substitution for the clozapine stimulus, also resulted in the detection of clozapine and its secondary metabolite, N‐desmethylclozapine. Importantly, the emergent levels of clozapine were equivalent to those previously shown to exert behavioral effects. Together, these data demonstrate that CNO is a behaviorally active compound in both mice and rats lacking DREADD receptors and trained to discriminate clozapine. Our results, along with recent findings by others, emphasize the need for appropriate control groups in studies employing DREADDs.Support or Funding InformationDA039991, DA038453
Effects of (‐)‐Epigallocatechin gallate (EGCG) on proliferation and viability of Jurkat T‐cells treated with ethanol
Authors: Snitsarev Vladislav 
Published: November 2023

Adverse effects of ethyl alcohol (EtOH), the most abused substance, on the immune system are not fully understood. We hypothesized that Jurkat T‐lymphocytes (JTL) cell counts will decrease in the presence of alcohol, and that after 48h growing in increasing EtOH concentrations (0.001%‐50% v/v) would result in a simple dose‐response curve with defined IC50 for EtOH.The Countess automated cell counter was used to measure the number of JTL in the Trypan Blue exclusive manner. The dose‐response relationship for EtOH alone obtained was far from the expected sigmoidal or biphasic shape. First, cell count was significantly increased at 0.01% EtOH compared to control. Second, cell count remained the same at 5%, 10%, and 20% EtOH with no proliferation. This complex shape of the dose response curve indicates potential multiple effects of EtOH on JTL with possibly different mechanisms. To define the components of the dose‐response, further studies will be performed and more data points obtained to allow curve fitting. Live cells were also found at 30% EtOH but were uncountable by the Countess's image analysis because the media turned cloudy at this and higher EtOH concentrations. No live cells were detected at 50% EtOH.The EGCG concentration that can be achieved in plasma by drinking green tea is 10 μM. When 10 μM of EGCG was added 5 min before EtOH treatment, it abrogated the effects of 0.01% EtOH and shifted the IC50 for EtOH from 3% to 10%. At this point we conclude that protective effects of EGCG may be due to potential interactions with one or more pathways by which EtOH acts on Jurkat T‐cells.
N6‐Cyclohexyladenosine, an A1 Adenosine Receptor Agonist, as a Novel Thermolytic Adjunctive Pharmacotherapy for Targeted Temperature Management
Authors: Laughlin Bernard , Baily Isaac , Rice Sarah , Bararti Zeinab , Drew Kelly 
Published: November 2023

Targeted temperature management (TTM) previously known as therapeutic hypothermia, the lowering of core body temperature (Tb) over a 24h period, is a lifesaving and neuroprotective standard of care intervention for cardiac arrest and neonatal hypoxic ischemic encephalopathy. Prior work shows that the A1 Adenosine receptor (A1AR) agonist N6‐Cyclohexyladenosine (CHA), inhibits shivering and nonshivering thermogenesis and lowers core body temperature. However, an optimal delivery protocol has not been developed. Here our purpose is to optimize a CHA delivery protocol to achieve and maintain a predictable and consistent target Tb of 32°C over a 24h period and also to quantify and characterize physiological responses to CHA assisted cooling at a temperature range and cooling interval consistent with current evidence based guidelines for targeted temperature management in cardiac arrest.Sprague‐Dawley rats (n = 22) were instrumented with CTA‐F40 transmitters (DSI International) for continuous recording of Tb and ECG, arterial and venous cannulas and in some cases, brain cannula for monitoring brain temperature. Rats were administered CHA via continuous IV infusion or intraperitoneal injections to inhibit thermogenesis. In the first experiment ambient temperature was modulated to lower Tb with increasing doses of CHA to optimize cooling. In the second experiment cage surface temperature was modulated to control Tb with the CHA dose determined from the first experiment. Core body and brain temperatures, heart rate and rhythm, blood gas and electrolytes were monitored throughout the experimentsResults indicate a pronounced individual variation in response to CHA and the development of tolerance, necessitating a higher starting dose and use of dynamic conductive temperature modulation to prevent overcooling. We show that core body temperature predicts brain temperature during CHA induced cooling. CHA inhibits thermoregulatory shivering and core body temperature of 32°C can be safely maintained and modulated with surface cooling and continuous IV infusion of CHA over a 24h period. Acid‐base, electrolyte and blood gas analysis indicated acute hyperglycemia and a mild respiratory acidosis during the initiation of cooling. The hyperglycemia was transient and all rats were normoglycemic at the end of cooling and arterial pH normalized via metabolic compensation.Support or Funding InformationNIH R15 NS070779
Effect of Hydrogen Sulfide‐Releasing Compounds on Aqueous Humor Outflow Facility Under Different Perfusion Pressures
Authors: Robinson Jenaye , Mitchell Leah , Ngele Kalu , Opere Catherine , Ohia Sunny E , Njie‐Mbye Ya Fatou 
Published: November 2023

Hydrogen sulfide (H2S)‐releasing compounds have been reported lower intraocular pressure in rabbits and increase aqueous humor outflow facility in a porcine ocular anterior segment model, ex vivo. The aim of the present study was to investigate the pharmacological actions of L‐cysteine, a substrate for the biosynthesis of H2S, on aqueous humor outflow facility using the porcine ocular anterior segment model maintained under normal and elevated ocular perfusion pressure.MethodsPorcine ocular anterior segment explants were perfused with Dulbecco's Modified Eagle's Medium maintained at 37°C and gassed with 5% CO2 and 95% under a constant normal perfusion pressure of 7.35 mmHg or under an elevated perfusion pressure of 15 mmHg. Stabilized explants were exposed to L‐cysteine (1 nM – 1 μM) and outflow facility was monitored for 4 hours. Control experiments containing vehicle (0.1% saline) were run in parallel.ResultsUnder normal pressure conditions, L‐cysteine elicited a concentration‐dependent increase in aqueous humor outflow facility that reached a maximal effect at 100 nM [(150.6 ± 17.2% of basal; (p < 0.04)], an effect that lasted for a duration of four hours. Interestingly, under conditions of elevated perfusion pressure, L‐cysteine (100 nM) also significantly increased outflow facility reaching a maximal effect of 173.0 ± 23.0% of basal (p < 0.01).ConclusionWe conclude that L‐cysteine can increase aqueous humor outflow facility in the porcine anterior segment model in a manner that was independent of perfusion pressure. However, further studies are needed to determine the role of H2S in regulating aqueous humor outflow under these conditions.