bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effects of an Acute Bout of Controlled Breathing on Short‐Term Heart Rate Variability
Authors: Hartman Sarah Roise , Wurtz Brendan , Aytes Caleb , Marley Emma , Sergent Madison , Kieffer H. Scott 
Published: April 2020

Heart rate variability (HRV) is a non‐invasive measurement of the autonomic nervous system (ANS) which uses the frequency and time domains of an ECG to determine the magnitude of sympathetic and parasympathetic activity. Decreased HRV has been associated with several disease conditions whereas increased HRV indicates increased parasympathetic drive, which attenuates physiological and psychological stress conditions. The short‐term HRV, 5‐minute, average, denotes the temporal and dynamic functioning of the ANS and can be used to monitor acute changes in allosteric load.ObjectiveTo determine the effect of an acute bout of controlled breathing on the frequency and time domain measures of HRV.MethodsTwenty‐nine subjects (19.4 ± 0.8 yrs) volunteered for the meditation activity. The subjects attended a familiarization session to give informed consent, adjust to the lab setting, and to practice a guided breathing technique, 5 breaths/min (4 second inhale, 2 second hold, 6 second exhale). The subjects returned to the lab for a 15‐minute experimental protocol during which, they sat quietly breathing normal for 5 minutes to establish a baseline, followed by 5 minutes of the guided breathing protocol and finishing the protocol with 5 minutes of normal breathing.The ECG recorded continuously over the 15‐minute protocol using a Polar H10 heart rate monitor. The raw data was downloaded into a commercially available HRV software program and the 5‐minute average for heart rate (HR), low frequency (LF), high frequency (HF), peak HF/LF ratio, and root mean square of the standard deviation (rMSSD) were calculated for baseline, guided breathing and recovery periods.Results5 minutes of guided breathing elicited significant differences in measures within the frequency domain (HF and LF) and the time domain (rMSSD) heart rate variability. HF baseline was 52.4 ± 20.9 nu significantly decreased to 18.8 ±10.1 nu following controlled breathing, and significantly increased to 36.6 ± 13.3 nu during the recovery. LF baseline was measured at 48.6 ± 22.6 nu, increased to 81.2 ± 10.1 nu during controlled breathing and returned to 63.4 ± 17.3 nu during recovery. The rMSSD baseline was 64.9 ± 36.4. It increased significantly by 18.9% to 79.6 ± 37.8 and returned to baseline measures 60.7 ± 35.7 following the breathing exercise.DiscussionThe frequency domains of HF (parasympathetic) and LF (sympathetic) appear to respond in the opposite direction from the anticipated change in parasympathetic activity; however, these changes are indicative of slow controlled breathing. Within the time domain rMSSD has been identified as an indicator of short‐term parasympathetic activity, specifically vagal nerve activation. The rMSSD results demonstrated that controlled breathing provided significant parasympathetic response during the controlled breathing technique; however, the acute increase in activity was not sustainable past the breathing intervention.
High Fat Diet versus Disturbed Blood Flow Conditions: Implications for Endothelial Glycocalyx Integrity and Pre‐Atherosclerotic Inflammation
Authors: Mitra Ronodeep , Qiao Ju , Madhavan Sudharsan , O’Neil Gerard , Ritchie Bailey , Kulkarni Praveen , Sridhar Srinivas , van de Ven Anne , Cherry Erica , Ferris Craig , Hamilton James , Ebong Eno 
Published: April 2020

IntroductionEndothelial glycocalyx (GCX) shedding plays a role in endothelial dysfunction and increases vessel wall permeability to inflammatory cells contributing to atherogenesis. We sought to determine whether a high fat diet (HFD) or disturbed blood flow conditions, both well‐known atherogenic risk factors, would more detrimentally contribute to pre‐atherosclerotic loss of GCX integrity and vascular inflammation.Materials and MethodsC57BL/6‐background apolipoprotein E knockout (ApoE‐KO) mice were fed either a HFD or chow diet, and/or underwent a ligation of the left carotid artery (LCA), inducing disturbed flow conditions. After one week, mice were sacrificed and LCAs and right carotid arteries (RCAs) were preserved to compare GCX coverage and thickness and inflammatory macrophage accumulation in carotid arterial walls amongst and between cohorts.Results and DiscussionEndothelial GCX damage occurred in LCAs of HFD fed mice when compared to the control. More significant GCX damage occurred in the LCAs of mice exposed to disturbed flow by partial LCA ligation, also compared to control. Flow simulations conducted through SimVascular adequately characterized flow patterns, pressure, and wall shear stresses in non‐ligated vs. ligated mice. They confirmed the notion that the LCA partial ligation surgery does indeed reduce wall shear stress and increase pressure, characteristics of disturbed flow. No difference in macrophage accumulation in carotid arterial walls was observed when comparing the LCAs of control mice to the LCAs of HFD fed mice. However, macrophage infiltration in vessel walls showed a 20‐fold increase in LCAs exposed to disturbed flow following ligation, when compared to control LCAs.ConclusionsThis study was the first to demonstrate that disturbed flow contributes more detrimentally to pre‐atherosclerotic loss of GCX integrity and vascular inflammation. The study concluded that disturbed flow conditions induced by partial ligation, compared to HFD conditions, compromised the integrity of the endothelial GCX to a greater extent. We anticipate more rapid atherogenesis as a consequence of the severity of this flow induced GCX damage.Support or Funding InformationWe are pleased to acknowledge that this work was funded by the National Institute of Health (NIH) K01‐ HL125499 awarded to E Ebong, NIH R21‐DA042583 awarded to S Sridhar, and Air Force Office of Scientific Research (AFOSR) FA2386‐17‐1‐4042 awarded to S Sridhar.
Does Hypoxia Affect Pulse Transit Time in Healthy Controls?
Authors: Brubaker Justin M , Carter Katrina J , Ward Aaron T , Kellawan J. Mikhail , Harrell John W , Eldridge Marlowe W , Roldan Alejandro , Wieben Oliver , Schrage William G 
Published: April 2020

Hypoxia is known to increase cerebral blood flow and increase sympathetic nervous activity (SNA). Given the strong link between elevated vascular stiffness and cardiovascular diseases exhibiting elevated SNA, we tested whether a hypoxic stressor in healthy subjects would acutely change cerebral vascular stiffness. We hypothesized hypoxia would lead to increased cerebrovascular stiffness as measured by a reduced pulse wave transit time. Eight healthy controls (31±8 yrs, M=3, F=5), with a BMI of 18.5 – 25 kg/m2, laid supine in a MRI, breathing room air (Normoxia) for ~10 minutes followed by a hypoxia condition, in which subjects breathed a gas mixture of 11% O2 and 89% nitrogen through a mouthpiece. Inspired CO2 between 1 – 5% of inspired air was bled in to maintain a constant end‐tidal CO2. Heart rate, end‐tidal CO2, arterial oxygen saturation, and blood pressure were continuously monitored. A 3 Tesla MRI using 4‐dimensional flow phase contrast vastly under‐sampled isotropic projection reconstruction (PC VIPR; ~6 minutes) was used to capture cerebral blood flow (CBF = blood velocity • vessel cross sectional area) in the internal carotid arteries (ICA) and superior sagittal sinus (SSS). Cerebral blood flow across 20 equal segments of the average cardiac cycle was used to determine the time to peak flow in the ICAs and SSS during normoxia and hypoxia. Pulse transit time (PTT) was calculated as the difference in time to peak in the SSS from the time to peak in the ICAs. Data were analyzed via paired t‐tests and are presented as mean ± SD. Significance was taken as p≤0.05. Per design, hypoxia decreased SpO2 from 98%±1 to 80%±5 and increased CBF from 642±122 to 747±150 ml/min (p<0.001), while end‐tidal CO2 did not change 40±2 and 39±2 mmHg. During normoxia, pulse transit time from ICA to SSS was 98±50 ms, whereas pulse transit time during hypoxia was 167±82 ms (one‐tailed P‐value=0.06). Contrary to our hypothesis, acutely increasing CBF with hypoxia led to increased pulse transit time between the ICA and SSS. These findings suggest conditions that increase cerebral blood flow may positively impact hemodynamics in a manner associated with decreased vascular stiffness.Support or Funding InformationADA 1‐12‐IN‐39
Are We Teaching to the Test? Medical Student Perceptions of the USMLE Step 1 Exam
Authors: Loder Danielle 
Published: April 2020

With many medical schools having undergone significant curricular reform, including those who have transitioned to a pass/fail curriculum model, residency programs have little quantitative data with which to compare individual medical students who apply to their programs. For these programs, the primary source of quantitative data is a student’s USMLE Step 1 exam score, because it provides a common measurement across medical schools with different curricula. This circumstance puts an immense amount of pressure on this one exam, sparking discussions at medical schools across the nation about the “Step 1 Climate” (
Chen et. al., 2019). In 2016, Indiana University School of Medicine – Bloomington (IUSM‐BL) underwent curricular reform. The new curriculum uses a pass/fail system for all courses. Given the emphasis placed on the Step 1 exam, I am interested in learning more about student perceptions of the Step 1 exam, specifically how it impacts their relationship with the IUSM‐BL curriculum.First‐ and second‐year medical students at IUSM‐BL were interviewed using a 30–60‐minute semi‐structured interview format. The questions were designed to obtain student perceptions of the USMLE Step 1 exam and its relationship to the current medical school curriculum at IUSM‐BL. Interview questions included the following: 1) Having students explain the Step 1 exam and its importance in their future education, 2) Explanations of how students are studying for the Step 1 exam, 3) Perceptions of how well the IUSM‐BL curriculum is preparing students for the Step 1 exam. A thematic analysis of the interview transcripts was performed to determine commonalities in responses. Resultant themes indicate that the USMLE Step 1 exam is ever‐present in the minds of our medical students. They stress the overemphasis on this exam for their future residency applications, and suggest some ideas for ways to alleviate the emphasis placed on the Step 1 exam. This study will contribute to answering the larger questions surrounding the effect of the Step 1 exam on students and medical education.
High‐resolution Epigenome Mapping Reveals Distinct and Divergent Roles for UHRF1 in the Maintenance of DNA Methylation
Authors: Tiedemann Rochelle L. , Du Qian , Dickson Bradley M. , Kong Xiangqian , Chomiak Alison A. , Zhou Wanding , Johnson Benjamin K. , Baylin Stephen B. , Jones Peter A. , Clark Susan J. , Rothbart Scott B. 
Published: April 2020

The E3 ubiquitin ligase UHRF1 is an established cofactor for replication‐coupled DNA methylation inheritance. Our group and others have made recent progress dissecting biochemical mechanisms linking UHRF1 to DNA methylation control. Our current model posits a step‐wise pathway in which UHRF1 engages nucleosomes through histone and DNA binding. This multivalent nucleosome readout directs UHRF1 ubiquitin ligase activity toward the N‐terminal tail of histone H3, a binding site for DNMT1. While this elegant chromatin regulatory process is now taking shape, it remains unclear whether the reliance on UHRF1 for DNA methylation maintenance is localized or genome‐wide. Here we present comparative, high‐resolution, genome‐scale analysis of DNA methylation maintenance following acute depletion of UHRF1 and DNMT1 in a human colorectal cancer cell line. As expected, DNMT1 depletion resulted in global reduction of DNA methylation genome‐wide. However, depletion of UHRF1 revealed distinct attributes of the genome that rely on UHRF1 for DNA methylation maintenance. Significantly, these distinct genomic attributes are divergent on their dependency of ubiquitin deposition on the histone H3 tail by UHRF1 to recruit DNMT1 and maintain DNA methylation. Notably, these newly identified UHRF1‐ubiquitin dependent DNA methylation signatures are consistent with the observed loss of DNA methylation that occurs during aging and cancer progression. We propose that UHRF1 misregulation is a key contributor to DNA methylation erosion that occurs through human lifespan and cancer.Support or Funding InformationThis work was supported by the Van Andel Institute, and grants from the National Institutes of Health to S.B.R. (R35GM124736) and the American Cancer Society ‐ Michigan Cancer Research Fund to R.L.T. (PF‐16‐245‐01‐DMC).
Jurkat T‐cells chronically growing at acidic pH 7.2 show increased CO2 hydration activity
Authors: Snitsarev Vladislav , Vega Quinn C. , Petroff Elena 
Published: April 2020

In our previous study (Vega et al. Faseb J. 32, S787.14) we reported that a clone of Jurkat T‐cell line that we have been chronically propagating at pH 7.2 (10% CO2) showed a significantly different growth pattern than the control clone at pH 7.4 (5% CO2).Since carbonic anhydrase (CA) is a key contributor to cellular pH regulation, here we tested if pH7.2 and pH7.4 clones have a different CA activity that was measured with the Wilbur‐Anderson assay; briefly, one unit is defined as 2*(T0‐T)/T, where T0 and T are the times in seconds in the absence and presence of enzyme, respectively, required for a saturated CO2 solution (4 mL) to lower pH of 20 mM TRIS buffer (6 mL) from 8.3 to 6.3 at 0°C.In a control experiment, CA with the reported activity (≥ 3,000 units/mg dry weight) showed in duplicate experiments 3,048 (T0=50.5 sec, T=10.5 sec, 0.0025 mg, determined with Hanna HI10832) and 3,111 (T0=66 sec, T=13.5 sec, 0.0025 mg, determined with a timer).To avoid the osmotic shock to the cells, we added 0.85% NaCl to all the assay’s solutions and tested if the presence of 0.85% NaCl affects CA activity.In the presence of 0.85% NaCl of NaCl, the values were 1,869±95 (T0=72.3±0.9 sec, T=21.8±0.8 sec, n=5), both blank T0 and enzyme T times being slower most likely because CO2 content in the saturated aqueous solution was smaller due to the presence of another solute, 0.85% NaCl.For the experiment, cell suspensions were span twice in the TRIS (20 mM)+NaCl 0.85% buffer at 0°C to achieve 1 mL of 10 million cells/mL density that was added to 5 mL of the TRIS buffer (pH 8.3), then immediately 4 mL of 0.85% NaCl saturated with CO2 was added, and time for pH to drop from 8.3 to 6.3 was measured; the final cell count being 10 million/mL in 10 mL of the reaction volume.For the pH7.4 clone, T= 82.3±1.1 sec (n=6) was slower than blank determination in 0.85% NaCl resulting in the apparent negative CA activity of −0.24 formally calculated as 2*(T0‐T)/T; while for the pH7.2 clone, the T= 77.3±1.4 sec (n=6) resulted in −0.13 (p<0.05).If the increased CO2 hydration in the pH7.2 clone is caused by the increase in CA molecules alone, we would expect that these cells would have an additional 0.11/(10*106 cells)/(3000 units/mg)/(1000 mg/g)/(30,000 g/mole) * 6.022*1023 = 7.4*104 CA molecules per cell.We conclude that 1) isotonic NaCl significantly inhibits apparent CA activity in the context of Wilbur‐Anderson assay units, 2) both pH7.2 and 7.4 clones at 1 million/mL cell density inhibited CO2 hydration compared to the blank CO2 hydration in the Wilbur‐Anderson assay supplemented with 0.85% NaCl; 3) in relation to each other, pH7.2 clone has a higher CO2 hydration activity than pH7.4 clone speculatively due to estimated additional 7.4*104 CA molecules.Differential CA activity and expression in the pH7.2 and 7.4 clones will be further compared using physiology and molecular biology tools.
Changes in Cellular Composition of Dentate Gyrus in Response to Intermittent Hypoxia
Authors: Nallamothu Thara , Castro-Rivera Carolina , Vera Adrianna , Garcia Alfredo J. 
Published: April 2020

Adult neurogenesis allows for the continual generation of neurons throughout adulthood. It is implicated in the maintenance of normal hippocampal function and is tightly regulated by oxygen homeostasis. Sleep apnea causes periodic cessations in breathing and leads to intermittent hypoxia (IH), which can impair hippocampal based learning and memory. This ongoing study examines how IH influences neural precursors and remodels the neurogenic niche in the hippocampus. We hypothesize that IH destabilizes the pool of intermediate neural progenitors (INPs) and recruits microglia into the area. Our findings indicate that the number of INPs is reduced by IH. Moreover, while IH does not change the number of microglia in the molecular and granular layers of the dentate gyrus, microglia appear to be uniquely recruited into the neurogenic niche (i.e., the subgranular zone) following IH. These findings suggest that IH‐dependent changes in hippocampal adult neurogenesis may stimulate microglial activity which in turn further impact normal hippocampal function. Such effects may play a significant role in influencing hippocampal physiology during untreated sleep apnea.Support or Funding InformationThis work was supported by NIH PO 1 HL 144454, NIH R01 NS10742101 awarded to AJG, and a grant from The BSD Office of Diversity & Inclusion at The University of Chicago awarded to AJG.
A Putative Cystathionine Beta‐Synthase Homolog of Mycobacterium smegmatis is Involved in de novo Cysteine Biosynthesis
Authors: Mahato Saroj Kumar , Saini Jasleen , Barabote Ravi Damodar 
Published: April 2020

Mycobacteria include serious pathogens of humans and animals. Mycobacterium smegmatis is a non‐pathogenic model that is widely used to study core mycobacterial metabolism. Using M. smegmatis, we are genetically investigating mycobacterial pathways for biosynthesis of cysteine, a vital sulfur‐containing amino acid.
Publishedin vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM. However, in vivo data were lacking. The M. smegmatis genome encodes only a CysM homolog and lacks orthologs for CysK1 or CysK2. However, the genome encodes a putative cystathionine beta‐synthase (CBS) protein that has two domains ‐ an N‐terminal domain that shares weak sequence similarity with CysK1 and a C‐terminal domain that is specific to CBS enzymes. CBS is a metabolic enzyme that catalyzes the conversion of homocysteine to cystathionine in all the three domains of life (Bacteria, Archaea, and Eukarya).
To dissect the roles of CysM and CBS proteins in cysteine biosynthesis in vivo, we generated a series of unmarked gene deletion mutants and gene complementation strains of M. smegmatis and analyzed them phenotypically. We found that neither the ΔcysM nor the Δcbs mutants of M. smegmatis were auxotrophic for cysteine. However, a ΔcbsΔcysM double mutant of M. smegmatis was auxotrophic for cysteine. Genetic complementation of the double mutant using either cbs or cysM genes rescued cysteine auxotrophy. Furthermore, the N‐terminal CysK1‐like domain of the putative CBS was sufficient to rescue cysteine auxotrophy. Thus, our in vivo data implicate a role for the putative CBS in cysteine biosynthesis and also suggest that the protein may have dual functions in mycobacteria.
Multidrug resistant (MDR) strains of M. tuberculosis, the causative agent of Tuberculosis (TB), are becoming a global crisis. Mycobacterial sulfur metabolism has emerged as a vital target for developing novel drugs to treat MDR‐TB. Our findings reveal a potentially new target in mycobacterial sulfur metabolism relevant to strategic development of novel TB drugs.Support or Funding InformationThis project was supported by the Cell and Molecular Biology program and the Department of Biological Sciences at the University of Arkansas, Fayetteville, AR 72701.
A Geometric Morphometric Evaluation of Equid Tooth Shape at Natural Trap Cave, Wyoming
Authors: Grass Andy , Jones Jade , Campbell Anna , Higgins Penny , Meachen Julie 
Published: April 2020

Natural Trap Cave is a sinkhole cave located in Big Horn County in northern Wyoming. The cave preserves many Quaternary taxa, including pollen and large carnivorous and herbivorous mammals such as various felids and ungulates. Many of these taxa went extinct in North America following the late Pleistocene megafaunal extinction. The cave was first excavated in the 1970s and 80s by teams from the University of Kansas and the University of Missouri, and more recently by teams from Des Moines University, The University of Adelaide, and The University of Rochester, along with a wide variety of volunteers. Specimens from this cave have been used to elucidate floral change in the area, disentangle ancient food webs, and extend the hypothesized range for Beringian wolves.Horses are the most common megafaunal group from this site, encompassing two genera: Equus and Haringtonhippus, the “New World stilt‐legged” horse, based on post‐cranial elements and mitochondrial DNA. Some recent studies have shown that horse taxa can be identified by tooth occlusal surface morphology. This study aims to test if isolated equid cheek teeth from Natural Trap Cave can be identified to the genus level, between Equus and Haringtonhippus using geometric morphometrics. 2D landmarks and sliding semi‐landmarks were taken around the periphery of a set of upper cheek teeth, including the areas of greatest curvature at the metastyle, mesostyle, parastyle, and around the protocone and post protoconal valley. Principal component analyses on known specimens do in fact separate Equus and Haringtonhippus, and this difference is statistically sigificant, with the primary difference being the width of the protocone. Additionally, molars and premolars also occupied significantly different areas of morphospace, opening up the possibility of identifying tooth position on unknown specimens as well. With the abundance of isolated horse teeth (either Equus or Haringtonhippus) from Natural Trap Cave, having a reliable means to distinguish between genera will allow us to better study the ecological differences between them and better understand the environment and faunal interactions in late Pleistocene Wyoming.Support or Funding InformationNSF EAR/SGP 1425059 (Natural Trap Cave Revisited: Ancient DNA, Climate and the Megafaunal Extinction) Julie Meachen, PI