bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paper Charts
Authors: Frost Emma D. , Donlon Jack , Mitwally Aimin , Magnani Gretchen , Tomlin Shay , Berk Michael , Koola Maju Mathew 
Published: January 2023

Abstract
The use of electronic medical records (EMRs) has increased dramatically over the last 15 years. However, psychiatry has lagged. EMRs are not being used by many mental health professionals. There are many reasons, including financial burden, lack of technological support, stigma, disaggregation of upfront costs, indirect benefits, and concerns about privacy and Health Insurance Portability and Accountability Act compliance. Obtaining paper records is a lengthy process, making continuity of care and emergency care challenging. Even when records are made available, it is common for information to be incomplete. The objective of this article is to highlight how the continued use of paper charts may decrease the quality and timeliness of psychiatric care provided and to discuss the psychiatry-specific issues created by EMRs. A case illustrating the disruption of care by continued use of paper charts in psychiatric facilities is presented. The growing use of EMR creates new challenges that affect psychiatry in ways other fields are not affected. These challenges include confidentiality issues, the frequent change/spectrum of diagnoses, determining how much information should be recorded in a note, and what the implications are of the information recorded. This article will discuss the use of EMRs in psychiatry, as well as encourage medical students and residents to take a deeper dive into psychiatry-specific issues regarding the use of EMR. EMR use may have a profound impact on our patient outcomes, health care delivery system, shorter inpatient stay, as well as reduce health care costs.
Opioid Use in Pregnancy: A Review
Authors: Ryan Kimberly S. , Prewitt Kristin C. , Hayer Sarena , Hedges Madeline A. , Benson Ashley E. , Lo Jamie O. 
Published: January 2023

Importance
The use and misuse of opioids in pregnancy have been increasing and are a major public health issue. Opioid use in pregnancy and during lactation has been associated with increased maternal and neonatal morbidity and mortality.

Objective
This review aims to summarize the existing literature and current recommendations for opioid use while pregnant or lactating.

Evidence Acquisition
A PubMed, Cochrane Library, and Google Scholar literature search using the following terms was performed to gather relevant data: “opioids,” “opioid maintenance therapy,” “opioid use disorder,” “suboxone,” “buprenorphine,” “methadone,” “medication for opioid use disorder,” “fetal outcomes,” “perinatal outcomes,” “pregnancy,” “lactation,” and “neonatal abstinence syndrome.”

Results
Available studies on opioid use in pregnancy and during lactation were reviewed and support association with increased odds of maternal death, placental insufficiency, cardiac arrest, preterm birth, neonatal intensive care unit admission, low birth weight, and small for gestational age infants. Studies were also reviewed on pharmacotherapy options in pregnancy and promising prenatal care models.

Conclusion and Relevance
There is a critical need for research on the effects of opioid use and related pharmacotherapy options in pregnancy. Once the adverse perinatal effects of opioid exposure are identified and well-characterized, patient education, intervention, and antenatal surveillance can be developed to predict and mitigate its impact on maternal and fetal health.

Target Audience
Obstetricians and gynecologists, family physicians.

Learning Objectives
After participating in this activity, the learner should be better able to propose patient counseling strategies regarding prenatal opioid use; explain patient assessment measures for opioid use during pregnancy; and discuss recommendations regarding opioid use while breastfeeding.
Estimated Incidence and Prevalence of Gonorrhea in the United States, 2006–2019
Authors: Pollock Emily D. , Clay Patrick A. , Kreisel Kristen M. , Spicknall Ian H. 
Published: January 2023

Background
We extend recent work estimating incidence and prevalence of gonococcal infections among men and women aged 15 to 39 years in the United States in 2018 by applying the same modeling framework to estimate gonococcal incidence and prevalence during 2006 to 2019.

Methods
The model is informed by cases from the Nationally Notifiable Disease Surveillance System, data from the National Survey of Family Growth, and data on other factors known to impact gonococcal incidence and prevalence. We use Monte Carlo simulation to account for uncertainty in input parameters. Results are reported as median annual per-capita incidence and prevalence; uncertainty intervals are characterized by the 25th and 75th simulated percentiles.

Results
There were 1,603,473 (1,467,801-1,767,779) incident cases of gonorrhea estimated in 2019. Per-capita incidence increased 32%, from 1101 (1002–1221) to 1456 (1333–1605) infections per 100,000 persons. This trend in per-capita incidence had 3 phrases: an initial decline during 2006 to 2009, a plateau through 2013, and a rapid increase of 66% through 2019. Men aged 25 to 39 years experienced the greatest increase in incidence (125%, 541 [467–651] to 1212 infections [1046–1458] per 100,000 men). Women aged 25 to 39 years had the lowest incidence in 2019, with 1040 infections (882–1241) per 100,000 women. Prevalence increased more slowly among those aged 25 to 39 years versus 15 to 24 years. The incidence ratio comparing men with women aged 25 to 39 years increased from 0.76 to 1.18.

Conclusions
The burden of gonorrhea has increased among men and women aged 15 to 39 years since 2013. An increasing proportion of incident infections are among men. Additional biomedical and behavioral interventions are needed to control gonococcal transmission.
Retrospective Analysis of Imaging Characteristics of Tectal Gliomas
Authors: Pokhylevych Halyna , Khose Swapnil , Amer Ahmad , Alhasan Hamza , Kaya Diana , Johnson Rashad , Fuller Greg , Gruschkus Stephen K. , Zaky Wafik , Weinberg Jeffrey S. , Johnson Jason M. 
Published: January 2023

Background and Purpose
Tectal gliomas (TGs) are rare tumors that involve critical locations in the brainstem, including the superior and inferior colliculi and the Sylvian aqueduct. The rarity of these tumors and the lack of large clinical studies have hindered adequate understanding of this disease. We sought to determine the association between imaging characteristics of TG and progression-free survival (PFS).

Materials and Methods
In this retrospective cohort study, impact of imaging characteristics (contrast enhancement, calcifications, cystic changes, presence of hydrocephalus) on survival was analyzed for 39 patients with TG. We used the Kaplan-Meier survival analysis method for determining the association between imaging characteristics and PFS. Progression-free survival was measured from time of diagnosis to radiographic or pathological disease progression during observation period. Progression was defined as more than 25% increase of the lesion in size, per response assessment in neuro-oncology, together with clinical deterioration and/or a need for intervention. Progression-free survival differences by various imaging characteristics were assessed using the log-rank test and univariable Cox proportional hazard regression. Because most of the studies in the current literature tend to overrepresent pediatric patients, we aimed to determine the association between TG tumors' imaging characteristics and PFS in both adult and pediatric patients. All statistical analyses were performed using STATA version 16.1 (Stata Corp, College Station, Tex).

Results
Of the 39 patients, radiographic tumor progression was observed in 15 cases (38.5%). Median PFS for 39 patients during observation was 21.8 years. Tectal gliomas that showed contrast enhancement initially or developed contrast enhancement during surveillance on magnetic resonance imaging had significantly lower PFS than those without (hazard ratio, 3.55; 95% confidence interval, 1.09–11.58; log-rank P value, 0.02).

Conclusions
Analysis of this patient population showed that contrast-enhancing TGs should not be categorically defined as benign lesions. This subgroup of patients should be followed closely for signs of progression.
DEVELOPMENT OF A MACHINE LEARNING MODEL FOR PREDICTING 28-DAY MORTALITY OF SEPTIC PATIENTS WITH ATRIAL FIBRILLATION
Authors: Wang Ziwen , Zhang Linna , Chao Yali , Xu Meng , Geng Xiaojuan , Hu Xiaoyi 
Published: January 2023

ABSTRACT

ABSTRACT

Introduction: Septic patients with atrial fibrillation (AF) are common in the intensive care unit accompanied by high mortality. The early prediction of prognosis of these patients is critical for clinical intervention. This study aimed to develop a model by using machine learning (ML) algorithms to predict the risk of 28-day mortality in septic patients with AF. Methods: In this retrospective cohort study, we extracted septic patients with AF from the Medical Information Mart for Intensive Care III (MIMIC-III) and IV database. Afterward, only MIMIC-IV cohort was randomly divided into training or internal validation set. External validation set was mainly extracted from MIMIC-III database. Propensity score matching was used to reduce the imbalance between the external validation and internal validation data sets. The predictive factors for 28-day mortality were determined by using multivariate logistic regression. Then, we constructed models by using ML algorithms. Multiple metrics were used for evaluation of performance of the models, including the area under the receiver operating characteristic curve, sensitivity, specificity, recall, and accuracy. Results: A total of 5,317 septic patients with AF were enrolled, with 3,845 in the training set, 960 in the internal testing set, and 512 in the external testing set, respectively. Then, we established four prediction models by using ML algorithms. AdaBoost showed moderate performance and had a higher accuracy than the other three models. Compared with other severity scores, the AdaBoost obtained more net benefit. Conclusion: We established the first ML model for predicting the 28-day mortality of septic patients with AF. Compared with conventional scoring systems, the AdaBoost model performed moderately. The model established will have the potential to improve the level of clinical practice.
Leveraging open tools to realize the potential of self-archiving: A cohort study in clinical trials
Authors: Franzen Delwen L. 
Published: January 2023

AbstractWhile Open Access (OA) is growing, many publications remain behind a paywall. This limits the impact of research and entrenches global inequalities by restricting access to knowledge to those that can afford it. Many journal policies allow researchers to make a version of their publication openly accessible through self-archiving in a repository, sometimes after an embargo period (green OA). Unpaywall and Shareyourpaper are open tools that help users find OA articles and support authors to legally self-archive their papers, respectively. This study leveraged these tools to assess the potential of green OA to increase discoverability in a cohort of clinical trial results publications from German university medical centers. Of the 1,897 publications in this cohort, 46% (n=871/1,897, 95% Confidence Interval (CI) 44% to 48%) were not openly accessible via a journal or a repository. Of these, 85% (n=736/871, 95% CI 82% to 87%) had a permission to self-archive the accepted or published version in an institutional repository. Thus, most of the closed-access clinical trial results in this cohort could be made openly accessible, in line with World Health Organization (WHO) recommendations. In addition to providing further evidence of the unrealized potential of green OA, this study demonstrates the use of open tools to obtain actionable information on self-archiving at scale, and empowers efforts to increase science discoverability.
Self-experience in MDMA assisted therapy of PTSD
Authors: van der Kolk Bessel A. , Wang Julie B. , Yehuda Rachel , Bedrosian Leah , Cooker Allison , Harrison Charlotte , Mithoefer Michael , Yazar-Klosinki Berra , Emerson Amy , Doblin Rick 
Published: January 2023

AbstractIn recent years there has been a resurgence of interest in the therapeutic potential of psychedelic substances such as 3,4-methylenedioxymethamphetamine (MDMA). This renaissance of psychedelic studies opens the door for a new paradigm in psychiatric medicine: drug-facilitated psychotherapy. In this study we report the findings of a randomized, double-blind, placebo-controlled, multi-site Phase 3 clinical trial (NCT03537014) to test the effects of MDMA-assisted therapy (MDMA-AT) on patients with severe PTSD. The vast majority (85%) of individuals in this study reported having suffered early childhood trauma, which is strongly associated with deficits in emotional coping skills /altered self-capacities, which have been shown to constitute major obstacles to successful completion of currently available evidence-based treatments. Partcicipants were randomized 1:1 to receive manualized therapy with either MDMA or placebo with three preparatory and nine integrative therapy sessions. Symptoms were measured at baseline and at 2□ months after the last experimental session with the Clinician-Administered PTSD Scale for DSM-5, the Toronto Alexithymia Scale (TAS_20), the Self Compassion Scale (SCS) and the Inventory of Altered Self-Capacities (IASC). MDMA-AT, compared with psychotherapy alone, significantly altered the domains of alexithymia, self-compassion, and altered self-capacities. These findings suggest that MDMA-AT can substantially improve transdiagnostic mental processes associated with poor treatment response.
Evolution of explorative and exploitative search strategies in collective foraging
Authors: Garg Ketika , Smaldino Paul E. , Kello Christopher T. 
Published: January 2023

AbstractEvolutionary theories of foraging hypothesize that foraging strategies evolve to maximize search efficiency. Many studies have investigated the central trade-off between explore-exploit and how individual foragers manage it under various conditions. For foragers in groups, this trade-off can be affected by the social environment, influencing the evolution of individual search strategies. Previous work has shown that when learning socially, explorative search strategies can optimize group search efficiency. However, social learning can cause discrepancies in strategies that benefit the group vs. an individual. We model the evolution of explorative and exploitative strategies using Lévy exponents under different levels of social learning and investigate their effect on individual and group search efficiencies. We show that reliance on social learning can lead to the evolution of mixed groups that are not optimally efficient. Exploiters can have a selective advantage in scrounging findings by explorers, but too many exploiters can diminish group efficiencies. However, greater opportunities for social learning can increase the benefits of explorative strategies. Finally, we show that area-restricted search can help individuals balance exploration and exploitation, and make groups more efficient. Our results demonstrate how exploration and exploitation must be balanced at both individual and collective levels for efficient search.
GolpHCat (TMEM87A): a unique voltage-gated and pH-sensitive cation channel in the Golgi
Authors: Kang Hyunji , Jeong Heejin , Han Ah-reum , Koh Wuhyun , Lee Jung Moo , Jo Heeyoung , Lee Hayeon , Bhalla Mridula , Roh Woo Suk , Jang Hyun Jun , Lee Boyoung , Kim Ho Min , An Hyun Joo , Lee C. Justin 
Published: January 2023

AbstractThe Golgi apparatus is a critical intracellular organelle that is responsible for modifying, packaging, and transporting proteins to their destinations. Golgi homeostasis involving the acidic pH, ion concentration, and membrane potential, is critical for proper functions and morphology of the Golgi. Although transporters and anion channels that contribute to Golgi homeostasis have been identified, the molecular identity of cation channels remains unknown. Here we identify TMEM87A as a novel Golgi-resident cation channel that contributes to pH homeostasis and rename it as GolpHCat (GolgipH-sensitiveCation channel). The genetic ablation of GolpHCat exhibits an impaired resting pH in the Golgi. Heterologously expressed GolpHCat displays voltage- and pH-dependent, non-selective cationic, and inwardly rectifying currents, with potent inhibition by gluconate. Furthermore, reconstitution of purified GolpHCat in liposomes generates functional channel activities with unique voltage-dependent gating and ion permeation. GolpHCat is expressed in various cell types such as neurons and astrocytes in the brain. In the hippocampus, GolpHCat-knockout mice show dilated Golgi morphology and altered glycosylation and protein trafficking, leading to impaired spatial memory with significantly reduced long-term potentiation. We elucidate that GolpHCat, by maintaining Golgi membrane potential, regulates ionic and osmotic homeostasis, protein glycosylation/trafficking, and brain functions. Our results propose a new molecular target for Golgi-related diseases and cognitive impairment.
Phylogenetic comparative approach reveals evolutionary conservatism, ancestral composition, and integration of vertebrate gut microbiota
Authors: Perez-Lamarque Benoît , Sommeria-Klein Guilhem , Duret Loréna , Morlon Hélène 
Published: January 2023

AbstractHow host-associated microbial communities evolve as their hosts diversify remains equivocal: How conserved is their composition? What was the composition of ancestral microbiota? Do microbial taxa covary in abundance over millions of years? Multivariate phylogenetic models of trait evolution are key to answering similar questions for complex host phenotypes, yet they are not directly applicable to relative abundances, which usually characterize microbiota. Here, we extend these models in this context, thereby providing a powerful approach for estimating phylosymbiosis (the extent to which closely related host species harbor similar microbiota), ancestral microbiota composition, and integration (evolutionary covariations in bacterial abundances). We apply our model to the gut microbiota of mammals and birds. We find significant phylosymbiosis that is not entirely explained by diet and geographic location, indicating that other evolutionary-conserved traits shape microbiota composition. We identify main shifts in microbiota composition during the evolution of the two groups and infer an ancestral mammalian microbiota consistent with an insectivorous diet. We also find remarkably consistent evolutionary covariations among bacterial orders in mammals and birds. Surprisingly, despite the substantial variability of present-day gut microbiota, some aspects of their composition are conserved over millions of years of host evolutionary history.
Dissecting the respective roles of microbiota and host genetics in the susceptibility ofCard9-/-mice to colitis
Authors: Danne C. , Lamas B. , Lavelle A. , Michel M-L. , Da Costa G. , Pham Hang-Phuong , Lefevre A. , Bridonneau C. , Bredon M. , Planchais J. , Straube M. , Emond P. , Langella P. , Sokol H. 
Published: January 2023

AbstractBackgroundThe etiology of Inflammatory Bowel Disease (IBD) is unclear but involves both genetics and environmental factors, including the gut microbiota. Indeed, exacerbated activation of the gastrointestinal immune system toward the gut microbiota occurs in genetically susceptible hosts and under the influence of the environment. For instance, a majority of IBD susceptibility loci lie within genes involved in immune responses, such as caspase recruitment domain member 9 (Card9). However, the relative impacts of genotype versus microbiota on colitis susceptibility in the context of CARD9 deficiency remain unknown.ResultsCard9gene directly contributes to recovery from dextran sodium sulfate (DSS)-induced colitis by inducing the colonic expression of the cytokine IL-22 and the antimicrobial peptidesReg3βandReg3γindependently of the microbiota. On the other hand,Card9is required for regulating the microbiota capacity to produce AhR ligands, which leads to the production of IL-22 in the colon, promoting recovery after colitis. In addition, cross-fostering experiments showed that five weeks after weaning, the microbiota transmitted from the nursing mother before weaning had a stronger impact on the tryptophan metabolism of the pups than the pups’ own genotype.ConclusionsThese results show the role of CARD9 and its effector IL-22 in mediating recovery from DSS-induced colitis in both microbiota-independent and microbiota-dependent manners.Card9genotype modulates the microbiota metabolic capacity to produce AhR ligands, but this effect can be overridden by the implantation of a WT or “healthy” microbiota before weaning. It highlights the importance of the weaning reaction occurring between the immune system and microbiota for host metabolism and immune functions throughout life. A better understanding of the impact of genetics on microbiota metabolism is key to developing efficient therapeutic strategies for patients suffering from complex inflammatory disorders.
TOBF1 modulates mouse embryonic stem cell fate through co-transcriptional regulation of alternative splicing
Authors: Aich Meghali , Ansari Asgar Hussain , Ding Li , Iesmantavicius Vytautas , Paul Deepanjan , Choudhary Chunaram , Maiti Souvik , Buchholz Frank , Chakraborty Debojyoti 
Published: January 2023

AbstractEmbryonic stem (ES) cells retain the ability to undergo lineage-specific differentiation that can eventually give rise to different cell types that constitute an organism. Although stem cell specific biological networks of transcription factors and epigenetic modifiers are well established, how the ES cell specific transcriptional and alternative splicing (AS) machinery regulate their expression has not been sufficiently explored. In this study, we show that the lncRNA associated protein TOBF1 regulates the co-transcriptional alternative splicing of transcripts necessary for maintaining stem cell identity in mouse ES cells. Overlaying information derived from TOBF1 chromatin occupancy, the distribution of its pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and alternative splicing upon its disruption unmasked local nuclear territories where these distinct events converge, ultimately leading to the maintenance of mouse ES cell identity.