bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cognitive Intra-individual Variability in the Laboratory Is Associated With Greater Executive Dysfunction in the Daily Lives of Older Adults With HIV
Authors: Ridgely Natalie C. , Woods Steven Paul , Webber Troy A. , Mustafa Andrea I. , Evans Darrian 
Published: October 2023

Background:
Executive dysfunction, which is common among persons with HIV (PWH), can have an adverse impact on health behaviors and quality of life. Intra-individual variability (IIV) is a measure of within-person variability across cognitive tests that is higher in PWH and is thought to reflect cognitive dyscontrol.

Objective:
To assess whether cognitive IIV in the laboratory is associated with self-reported executive dysfunction in daily life among older PWH.

Method:
Participants included 71 PWH aged ≥50 years who completed six subtests from the Cogstate battery and two subscales from the Frontal Systems Behavior Scale (FrSBe; self-report version). Cognitive IIV was calculated from the Cogstate as the coefficient of variation derived from age-adjusted normative T scores.

Results:
Cognitive IIV as measured by the Cogstate showed a significant, positive, medium-sized association with current FrSBe ratings of executive dysfunction but not disinhibition.

Conclusion:
Higher cognitive IIV in the laboratory as measured by the Cogstate may be related to the expression of HIV-associated symptoms of executive dysfunction in daily life for older PWH.
Analysis of Conflicts of Interest in Studies Related to Robotics in Gastrointestinal and Abdominal Wall Surgery
Authors: Jafar Uzair , Usama Muhammad , Hase Niklas E , Yaseen Haris , Nayyar Apoorve , Rabinowitz Judy B , Aziz Hassan 
Published: October 2023

BACKGROUND:
Industry payments to physicians represent a potential conflict of interest (COI) and can influence the study conclusions. This study aimed to evaluate the accuracy of the COIs reported in major surgical journals.

STUDY DESIGN:
Studies with at least one American author published between 2016 and 2021 that discussed observational and intervention studies assessing robotic surgery were included in the analysis. The Centers for Medicare & Medicaid Services’ Open Payments database was used to collect the industry payments. A COI is defined as receiving funding from a robotics company while publishing research directly related to the company’s products. A COI statement was defined as disclosed (or accurate) if the disclosure statement for the study in question acknowledged funding from the robotics companies. A COI was defined as undisclosed (or inaccurate) if the disclosure statement for the study in question did not acknowledge funding from the robotics companies.

RESULTS:
A total of 314 studies and 1978 authors were analyzed. Only 13.6% of the studies had accurate COI statements, whereas the majority (86.4%) had inaccurate COI disclosures. Additionally, 48.9% of the authors who received funding of $10,000 to $100,000 failed to report this amount in their disclosures, and 18% of the authors who received funding of $100,000 or more did not report it in their disclosures.

CONCLUSIONS:
There was a significant discordance between the self-reported COI in gastrointestinal and abdominal wall surgeries. This study calls for continued efforts to improve the definitions of what constitutes a relevant COI and encourages a standardized reporting process. It is imperative for investigators to make accurate disclosure statements.
Finding the Right Balance: Partial REBOA in a Swine Model of Uncontrolled Vascular Injury
Authors: Ho Jessie W , Dawood Zaiba Shafik , Nguyen Jessica , Diaz-Perez Dariel A , Taylor Meredith E , Chtraklin Kiril , Jin Guang , Liu Baoling , Ober Rebecca A , Alam Hasan B 
Published: October 2023

BACKGROUND:
We have previously shown that partial REBOA (pREBOA) deployment in the thoracic aorta is safe for 2 to 4 hours, but it is unclear whether the distal blood flow after partial aortic occlusion would lead to ongoing hemorrhage. The objective of this study was to evaluate the hemostatic efficacy of pREBOA in a model of uncontrolled vascular injury.

STUDY DESIGN:
Female Yorkshire swine (n = 10, 40 to 45 kg) were anesthetized and instrumented. A through-and-through injury was created in the common iliac artery. The animals were randomly assigned to: (1) pREBOA-PRO deployment after 3 minutes and (2) control. Both groups were given normal saline resuscitation for hypotension. The pREBOA was adjusted to partial occlusion (distal mean arterial pressure of 30 mmHg), and then left without titration for 2 hours. Then, fresh frozen plasma was transfused and the vessel repaired. The balloon was deflated and the animals were monitored for 2 hours. In the critical care period, 2 L of normal saline was infused, norepinephrine was given for mean arterial pressure ≤55, and electrolytes and acidosis were corrected. Organs were examined for gross and histologic evidence of ischemic injuries. The primary endpoint was post-inflation blood loss.

RESULTS:
All the pREBOA animals survived until the end, whereas control animals had a mean survival time of 38.2 minutes (p < 0.05). The pREBOA group showed significantly less bleeding after balloon deployment (93.8 vs 1,980.0 mL, p < 0.05), and had appropriate lactate clearance, with minimal histologic distal organ ischemia.

CONCLUSIONS:
Partial aortic occlusion with the newly designed balloon can achieve the desired balance between effective hemorrhage control and adequate distal flow, without a need for ongoing balloon titration.
Clinical Utility of Melanoma Sentinel Lymph Node Biopsy Nomograms
Authors: Drebin Harrison M , Hosein Sharif , Kurtansky Nicholas R , Nadelmann Emily , Moy Andrea P , Ariyan Charlotte E , Bello Danielle M , Brady Mary S , Coit Daniel G , Marchetti Michael A , Bartlett Edmund K 
Published: October 2023

BACKGROUND:
For patients with melanoma, the decision to perform sentinel lymph node biopsy (SLNB) is based on the estimated risk of lymph node metastasis. We assessed 3 melanoma SLNB risk-prediction models’ statistical performance and their ability to improve clinical decision making (clinical utility) on a cohort of melanoma SLNB cases.

STUDY DESIGN:
Melanoma patients undergoing SLNB at a single center from 2003 to 2021 were identified. The predicted probabilities of sentinel lymph node positivity using the Melanoma Institute of Australia, Memorial Sloan Kettering Cancer Center (MSK), and Friedman nomograms were calculated. Receiver operating characteristic and calibration curves were generated. Clinical utility was assessed via decision curve analysis, calculating the net SLNBs that could have been avoided had a given model guided selection at different risk thresholds.

RESULTS:
Of 2,464 melanoma cases that underwent SLNB, 567 (23.0%) had a positive sentinel lymph node. The areas under the receiver operating characteristic curves for the Melanoma Institute of Australia, MSK, and Friedman models were 0.726 (95% CI, 0.702 to 0.750), 0.720 (95% CI, 0.697 to 0.744), and 0.721 (95% CI, 0.699 to 0.744), respectively. For all models, calibration was best at predicted positivity rates below 30%. The MSK model underpredicted risk. At a 10% risk threshold, only the Friedman model would correctly avoid a net of 6.2 SLNBs per 100 patients. The other models did not reduce net avoidable SLNBs at risk thresholds of ≤10%.

CONCLUSIONS:
The tested nomograms had comparable performance in our cohort. The only model that achieved clinical utility at risk thresholds of ≤10% was the Friedman model.
Parallel on-chip micropipettes enabling quantitative multiplexed characterization of vesicle mechanics and cell aggregates rheology
Authors: Landiech Sylvain , Elias Marianne , Lapèze Pierre , Ajiyel Hajar , Plancke Marine , Laborde Adrian , Mesnilgrente Fabien , Bourrier David , Berti Debora , Montis Costanza , Mazenq Laurent , Baldo Jérémy , Roux Clément , Delarue Morgan , Joseph Pierre 
Published: October 2023

AbstractMicropipette aspiration (MPA) is one of the gold standards to quantify biological samples’ mechanical properties, which are crucial from the cell membrane scale to the multicellular tissue. However, relying on the manipulation of individual home-made glass pipettes, MPA suffers from low throughput and difficult automation. Here, we introduce the sliding insert micropipette aspiration (SIMPA) method, that permits parallelization and automation, thanks to the insertion of tubular pipettes, obtained by photolithography, within microfluidic channels. We show its application both at the lipid bilayer level, by probing vesicles to measure membrane bending and stretching moduli, and at the tissue level by quantifying the viscoelasticity of 3D cell aggregates. This approach opens the way to high-throughput, quantitative mechanical testing of many types of biological samples, from vesicles and individual cells to cell aggregates and explants, under dynamic physico-chemical stimuli.
Gene flow throughout the evolutionary history of a polymorphic and generalist clownfish
Authors: Schmid Sarah , Salvy Marianne Bachmann , Jimenez Alberto Garcia , Bertrand Joris A. M. , Cortesi Fabio , Heim Sara , Huyghe Filip , Litsios Glenn , Marcionetti Anna , O’Donnell James , Riginos Cynthia , Tettamanti Valerio , Salamin Nicolas 
Published: October 2023

ABSTRACTEven seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus onAmphiprion clarkii(Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sessile adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status ofA. clarkiihas been under debate. We used whole-genome resequencing data of 67A. clarkiispecimens spread across the Indian and Pacific Oceans to characterise the species’ population structure, demographic history, and colour polymorphism. We found thatA. clarkiispread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Moreover, edge populations exhibited more similar colouration patterns compared to central populations. However, we demonstrate that colour polymorphism is not associated with population structure, thus, colour phenotype is unreliable in assessing the taxonomic status ofA. clarkii. Our study further highlights the power of whole-genome comparative studies to determine the taxonomy of geographically wide-ranging and phenotypically diverse species, supporting the status ofA. clarkiias a single species.
Antidiabetic Drugs May Prevent Kidney Damage
Authors: Vattimo Maria de Fatima Fernandes , Silva Eloiza Oliveira , Ventura Sara , Lima Camila , Garcia Jessica , Maia Alessandra Oliveira , Gusmão Juliana Veloso , Vieira Guilherme Henrique Ferreira , Victoria Carla Djamila de Pina 
Published: October 2023

ABSTRACTIntroductionSodium-glucose cotransporter 2 inhibitors (SGLT2i) are a class of drugs that act as glucose reducers in patients with type 2 diabetes mellitus. Recent meta-analyses have shown that SGLT2i also prevent acute kidney injury (AKI) in diabetic patients. The aim of this study was to investigate the protective effect of canagliflozin an SGLT2i on AKI due to ischemia and reperfusion (I/R) in non-diabetic rats.MethodsMale Wistar rats weighing 250-300 g were divided into four groups: Control; SHAM (rats submitted to surgical simulation of renal ischemia); I/R: rats submitted to renal ischemia (bilateral clamping of the renal hilum for 30 minutes); CANA+I/R: I/R rats that received canagliflozin (30mg/kg, oral, gavage; 5 days before I/R). Renal function parameters were evaluated (serum creatinine [CrS], inulin clearance [Clin]; renal hemodynamics mean arterial pressure [MAP], renal blood flow [RBF], renal vascular resistance [RVR]); oxidative profile (urinary peroxides - FOX, lipid peroxidation - TBARS, urinary nitrate- NO) and thiols in renal tissue and expression of nuclear factor-erythroid 2 related factor 2 [Nrf2] protein.ResultsThe I/R group showed an increase in CrS and a reduction in inulin clearance, while the CANA+I/R group showed a reduction in serum creatinine and an increase in inulin clearance compared to the I/R group. In addition, the CANA+I/R group showed a decrease in oxidative metabolites (FOX and TBARS) and an increase in Nrf2 compared to the I/R group.ConclusionCanagliflozin treatment prevented the reduction in renal function induced by ischemia and reperfusion. In addition, there was a reduction in oxidative activity due to a decrease in oxidative metabolites and urinary peroxides and an increase in renal tissue thiols and Nrf-2, which is responsible for transcribing antioxidant activity. Therefore, the current study confirmed a relevant renoprotective effect of canagliflozin in the presence of renal ischemia.
Closed-Loop Estimation of Neurostimulation Strength-Duration Curve Using Fisher Information Optimization and Comparison With Uniform and Random Methods
Authors: Alavi Seyed Mohammad Mahdi 
Published: October 2023

AbstractBackgroundStrength-duration (SD) curve, rheobase and chronaxie parameters provide insights about the interdependence between stimulus strength and stimulus duration (or pulse width), and the neural activation dynamics such as the membrane time constant, which are useful for diagnostics and therapeutic applications. The existing SD curve estimation methods are based on open-loop uniform and/or random selection of the pulse widths.ObjectiveTo develop a method for closed-loop estimation of the SD curve.MethodIn the proposed method, after the selection of each pulse width through Fisher information matrix (FIM) optimization, the corresponding motor threshold (MT) is computed, the SD curve estimation is updated, and the process continues until satisfaction of a stopping rule based on the successive convergence of the SD curve parameters. The results are compared with various uniform methods where pulse widths are chosen in ascending, descending and random orders, and with methods with two and all non-uniform random pulse widths.Results160 simulation cases were run. The FIM method satisfied the stopping rule in 144 runs, and estimated the rheobase (chronaxie in parenthesis) with an average absolute relative error (ARE) of 1.73% (2.46%), with an average of 82 samples. At this point, methods with two and all random pulse widths, and uniform methods with descending, ascending and random orders led to 5.66% (20.27%), 2.15% (4.51%), 8.57% (54.96%), 3.52% (5.45%), and 2.19% (4.40%) AREs, which are greater than that achieved through the FIM method. In all 160 runs, The FIM method has chosen the minimum and maximum pulse widths as the optimal pulse widths.ConclusionsThe SD curve is identifiable by acquiring the SD data from the minimum and maximum pulse widths achieved through the FIM optimization. The SD data at random or uniform pulse widths from only the vertical area or lower plateau of the curve might not result in satisfactory estimation.SignificanceThis paper provides insights about pulse widths selection in closed-loop and open-loop SD curve estimation methods.
A Markovian dynamics forC. elegansbehavior across scales
Authors: Costa Antonio C. , Ahamed Tosif , Jordan David , Stephens Greg J. 
Published: October 2023

How do we capture the breadth of behavior in animal movement, from rapid body twitches to aging? Using high-resolution videos of the nematode wormC. elegans, we show that a single dynamics connects posture-scale fluctuations with trajectory diffusion, and longer-lived behavioral states. We take short posture sequences as an instantaneous behavioral measure, fixing the sequence length for maximal prediction. Within the space of posture sequences we construct a fine-scale, maximum entropy partition so that transitions among microstates define a high-fidelity Markov model, which we also use as a means of principled coarse-graining. We translate these dynamics into movement using resistive force theory, capturing the statistical properties of foraging trajectories. Predictive across scales, we leverage the longest-lived eigenvectors of the inferred Markov chain to perform a top-down subdivision of the worm’s foraging behavior, revealing both “runs-and-pirouettes” as well as previously uncharacterized finer-scale behaviors. We use our model to investigate the relevance of these fine-scale behaviors for foraging success, recovering a trade-off between local and global search strategies.SIGNIFICANCE STATEMENTComplex phenotypes, such as an animal’s behavior, generally depend on an overwhelming number of processes that span a vast range of scales. While there is no reason that behavioral dynamics permit simple models, by subsuming inherent nonlinearities and memory into maximally-predictive microstates, we find one forC. elegansforaging. The resulting “Markov worm” is effectively indistinguishable from real worm motion across a range of timescales, and we can decompose our model dynamics both to recover and discover behavioral states. Employing a simple form of substrate interactions, we connect postures to trajectories, illuminating how worms explore the environment. In more complex organisms, our approach can also link behaviors across time, from rapid muscular control to neuromodulation.
Developmentally dynamic changes in DNA methylation in the human pancreas
Authors: MacCalman Ailsa , De Franco Elisa , Franklin Alice , Flaxman Christine S. , Richardson Sarah J. , Murrall Kathryn , Burrage Joe ,   Barts Pancreas Tissue Bank (BPTB), Walker Emma M , Morgan Noel G. , Hattersley Andrew T. , Dempster Emma L. , Hannon Eilis J. , Jeffries Aaron R. , Owens Nick D. L. , Mill Jonathan 
Published: October 2023

ABSTRACTDevelopment of the human pancreas requires the precise temporal control of gene expression via epigenetic mechanisms and the binding of key transcription factors. We quantified genome-wide patterns of DNA methylation in human fetal pancreatic samples from donors aged 6 to 21 post-conception weeks. We found dramatic changes in DNA methylation across pancreas development, with >21% of sites characterized as developmental differentially methylated positions (dDMPs) including many annotated to genes associated with monogenic diabetes. An analysis of DNA methylation in postnatal pancreas tissue showed that the dramatic temporal changes in DNA methylation occurring in the developing pancreas are largely limited to the prenatal period. Significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small proportion of sites showing sex-specific DNA methylation trajectories across pancreas development. Pancreas dDMPs were not distributed equally across the genome, and were depleted in regulatory domains characterized by open chromatin and the binding of known pancreatic development transcription factors. Finally, we compared our pancreas dDMPs to previous findings from the human brain, identifying evidence for tissue-specific developmental changes in DNA methylation. To our knowledge, this represents the most extensive exploration of DNA methylation patterns during human fetal pancreas development, confirming the prenatal period as a time of major epigenomic plasticity.
Unveiling the evolutionary history of lingonberry (Vaccinium vitis-idaeaL.) through genome sequencing and assembly of European and North American subspecies
Authors: Hirabayashi Kaede , Debnath Samir C. , Owens Gregory L. 
Published: October 2023

AbstractLingonberry (Vaccinium vitis-idaeaL.) produces tiny red berries that are tart and nutty in flavour. It grows widely in the circumpolar region, including Scandinavia, northern parts of Eurasia, Alaska, and Canada. Although cultivation is currently limited, the plant has a long history of cultural use among indigenous communities. Given its potential as a food source, genomic resources for lingonberry are significantly lacking. To advance genomic knowledge, the genomes for two subspecies of lingonberry (V. vitis-idaeassp.minusand ssp.vitis-idaeavar. ‘Red Candy’) were sequenced andde novoassembled into contig-level assemblies. The assemblies were scaffolded using the bilberry genome (V. myrtillus) to generate chromosome-anchored reference genome consisting of 12 chromosomes each with total length 548.07 Mbp (contig N50 = 1.17 Mbp, BUSCO (C%) = 96.5%) for ssp.vitis-idaea, and 518.70 Mbp (contig N50 = 1.40 Mbp, BUSCO (C%) = 96.9%) for ssp.minus. RNA sequencing based gene annotation identified 27,243 genes on the ssp.vitis-idaeaassembly, and transposable element detection methods found that 45.82% of the genome was repeats. Phylogenetic analysis confirmed that lingonberry is most closely related to bilberry and is more closely related to blueberries than cranberries. Estimates of past effective population size suggested a continuous decline over the past 1–3 MYA, possibly due to the impacts of repeated glacial cycles during Pleistocene leading to frequent population fragmentation. The genomic resource created in this study can be used to identify industry relevant genes (e.g., flavonoid genes), infer phylogeny, and call sequence-level variants (e.g., SNPs) in future research.
Bisphenol S moderately decreases the expression of syncytiotrophoblast marker genes and induces apoptosis in human trophoblast lineages
Authors: Adu-Gyamfi Enoch Appiah , Salamah Joudi , Cheeran Elisha Ann , Lee Bum-Kyu 
Published: October 2023

AbstractBisphenol S (BPS) is currently used in the manufacturing of several household equipment such as water pipes and food containers. Hence, its entrance into the human body is almost inevitable. The presence of BPS in body fluids has been reported. However, its potential toxicity, especially on human placenta development and pregnancy progression, has not been explored. In this study, we assessed the impacts of BPS on self-renewal and differentiation potentials of placental stem cells, also known as trophoblast stem cells (TSCs), by exposing them to three different BPS concentrations during both self-renewal and differentiation of TSCs into syncytiotrophoblast (ST), extravillous trophoblast (EVT), and trophoblast organoids. Interestingly, BPS treatment did not affect the stemness, cell cycle and proliferation of the TSCs but it induced apoptosis in each trophoblast lineage. BPS altered the expression of several fusion-related genes. However, this alteration did not translate into significant morphological defects in the STs and organoids. Moreover, BPS did not impair the differentiation of TSCs into EVTs. These findings suggest that the presence of BPS at the feto-maternal interface may exaggerate trophoblast apoptosis and moderately inhibit the trophoblast fusion pathway to affect placenta development and pregnancy. Our study offers valuable insights into the potential toxicity of BPS on human placenta development, emphasizing the need for epidemiological assessment of the relationship between maternal serum levels of BPS and pregnancy complications.