bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of perioperative oral swallowing function with post-esophagectomy outcomes and nutritional statuses in patients with esophageal cancer
Authors: Matsumoto Sohei , Wakatsuki Kohei , Nakade Hiroshi , Kunishige Tomohiro , Miyao Shintaro , Aoki Satoko , Tsujimoto Akinori , Tatsumi Takanari , Soga Masahiro , Sho Masayuki
Published: April 2024

Dysphagia after esophagectomy is a serious complication; however, no method has been established to accurately assess swallowing function. We evaluated the association of swallowing function tests with patients’ post-esophagectomy complications and nutritional statuses. We retrospectively reviewed the data of 95 patients with esophageal cancer who underwent esophagectomy between 2016 and 2021. We performed perioperative swallowing function tests, including the repetitive saliva swallowing test (RSST), maximum phonation time (MPT), and laryngeal elevation (LE). Patients with recurrent laryngeal nerve palsy (RLNP) and respiratory complications (RC) had significantly lower postoperative RSST scores than patients without them; the scores in patients with or without anastomotic leakage (AL) were similar. Postoperative MPT in patients with RLNP was shorter than that in patients without RLNP; however, it was similar to that in patients with or without AL and RC. LE was not associated with any complications. Patients with an RSST score ≤2 at 2 weeks post-esophagectomy had significant weight loss at 1, 6, and 12 months postoperatively compared with patients with an RSST score ≥3. The proportion of patients with severe weight loss (≥20% weight loss) within 1 year of esophagectomy was significantly greater in patients with RSST scores ≤2 than in those with RSST scores ≥3. Multivariate analysis showed that an RSST score ≤2 was the only predictor of severe post-esophagectomy weight loss. RSST scoring is a simple tool for evaluating post-esophagectomy swallowing function. A lower RSST score is associated with postoperative RLNP, RC, and poor nutritional status.
Non-invasive imaging in acute decompensated heart failure with preserved ejection fraction
Authors: Dhont Sebastiaan , Verbrugge Frederik H , Verwerft Jan , Bertrand Philippe B
Published: April 2024

Non-invasive imaging plays an increasingly important role in emergency medicine, given the trend towards smaller, portable ultrasound devices, the integration of ultrasound imaging across diverse medical disciplines, and the growing evidence supporting its clinical benefits for the patient. Heart failure with preserved ejection fraction (HFpEF) provides a compelling illustration of the impactful role that imaging plays in distinguishing diverse clinical presentations of heart failure with numerous associated comorbidities, including pulmonary, renal, or hepatic diseases. While a preserved left ventricular ejection fraction might misguide the clinician away from diagnosing cardiac disease, there are several clues provided by cardiac, vascular, and lung ultrasonography, as well as other imaging modalities, to rapidly identify (decompensated) HFpEF. Congestion remains the primary reason why patients with heart failure (irrespective of ejection fraction) seek emergency care. Furthermore, comprehensive phenotyping is becoming increasingly important, considering the development of targeted treatments for conditions exhibiting HFpEF physiology, such as cardiac amyloidosis. Timely recognition in such cases has lasting implications for long-term outcomes.
Can wage transparency alleviate gender sorting in the labour market?
Authors: Bamieh Omar , Ziegler Lennart
Published: April 2024

A large share of the gender wage gap can be attributed to occupation and employer choices. If workers are not well informed about these pay differences, increasing wage transparency might alleviate the gender gap. We test this hypothesis by examining the impact of mandatory wage postings. In 2011, Austria introduced a policy that requires firms to provide a minimum wage offer in job postings. To compare the pay prospects of vacancies before and after the introduction, we predict posted wages using detailed occupation–firm cells, which explain about 75% of the variation in wage postings. While we estimate a substantial gender gap of 15 log points, mandatory wage postings do not affect gender sorting into better-paying occupations and firms.
Shared Features Underlying Compact Genomes and Extreme Habitat Use in Chironomid Midges
Authors: Nell Lucas A , Weng Yi-Ming , Phillips Joseph S , Botsch Jamieson C , Book K Riley , Einarsson Árni , Ives Anthony R , Schoville Sean D
Published: April 2024

Nonbiting midges (family Chironomidae) are found throughout the world in a diverse array of aquatic and terrestrial habitats, can often tolerate harsh conditions such as hypoxia or desiccation, and have consistently compact genomes. Yet we know little about the shared molecular basis for these attributes and how they have evolved across the family. Here, we address these questions by first creating high-quality, annotated reference assemblies for Tanytarsus gracilentus (subfamily Chironominae, tribe Tanytarsini) and Parochlus steinenii (subfamily Podonominae). Using these and other publicly available assemblies, we created a time-calibrated phylogenomic tree for family Chironomidae with outgroups from order Diptera. We used this phylogeny to test for features associated with compact genomes, as well as examining patterns of gene family evolution and positive selection that may underlie chironomid habitat tolerances. Our results suggest that compact genomes evolved in the common ancestor of Chironomidae and Ceratopogonidae and that this occurred mainly through reductions in noncoding regions (introns, intergenic sequences, and repeat elements). Significantly expanded gene families in Chironomidae included biological processes that may relate to tolerance of stressful environments, such as temperature homeostasis, carbohydrate transport, melanization defense response, and trehalose transport. We identified several positively selected genes in Chironomidae, notably sulfonylurea receptor, CREB-binding protein, and protein kinase D. Our results improve our understanding of the evolution of small genomes and extreme habitat use in this widely distributed group.
Duplicate Gene Expression and Possible Mechanisms of Paralog Retention During Bacterial Genome Expansion
Authors: Garber Arkadiy I , Sano Emiko B , Gallagher Amy L , Miller Scott R
Published: April 2024

Gene duplication contributes to the evolution of expression and the origin of new genes, but the relative importance of different patterns of duplicate gene expression and mechanisms of retention remains debated and particularly poorly understood in bacteria. Here, we investigated gene expression patterns for two lab strains of the cyanobacterium Acaryochloris marina with expanding genomes that contain about 10-fold more gene duplicates compared with most bacteria. Strikingly, we observed a generally stoichiometric pattern of greater combined duplicate transcript dosage with increased gene copy number, in contrast to the prevalence of expression reduction reported for many eukaryotes. We conclude that increased transcript dosage is likely an important mechanism of initial duplicate retention in these bacteria and may persist over long periods of evolutionary time. However, we also observed that paralog expression can diverge rapidly, including possible functional partitioning, for which different copies were respectively more highly expressed in at least one condition. Divergence may be promoted by the physical separation of most Acaryochloris duplicates on different genetic elements. In addition, expression pattern for ancestrally shared duplicates could differ between strains, emphasizing that duplicate expression fate need not be deterministic. We further observed evidence for context-dependent transcript dosage, where the aggregate expression of duplicates was either greater or lower than their single-copy homolog depending on physiological state. Finally, we illustrate how these different expression patterns of duplicated genes impact Acaryochloris biology for the innovation of a novel light-harvesting apparatus and for the regulation of recA paralogs in response to environmental change.
Age Deficits in Associative Memory Are Not Alleviated by Multisensory Paradigms
Authors: Badham Stephen P , Atkin Christopher , Stacey Jemaine E , Henshaw Helen , Allen Harriet A , Roberts Katherine L
Published: April 2024

Objectives

Age deficits in memory are widespread, this affects individuals at a personal level, and investigating memory has been a key focus in cognitive aging research. Age deficits occur in memory for an episode, where information from the environment is integrated through the senses into an episodic event via associative memory. Associating items in memory has been shown to be particularly difficult for older adults but can often be alleviated by providing support from the external environment. The current investigation explored the potential for increased sensory input (multimodal stimuli) to alleviate age deficits in associative memory. Here, we present compelling evidence, supported by Bayesian analysis, for a null age-by-modality interaction.

Methods

Across three preregistered studies, young and older adults (n = 860) completed associative memory tasks either in single modalities or in multimodal formats. Study 1 used either visual text (unimodal) or video introductions (multimodal) to test memory for name-face associations. Studies 2 and 3 tested memory for paired associates. Study 2 used unimodal visual presentation or cross-modal visual-auditory word pairs in a cued recall paradigm. Study 3 presented word pairs as visual only, auditory only, or audiovisual and tested memory separately for items (individual words) or associations (word pairings).

Results

Typical age deficits in associative memory emerged, but these were not alleviated by multimodal presentation.

Discussion

The lack of multimodal support for associative memory indicates that perceptual manipulations are less effective than other forms of environmental support at alleviating age deficits in associative memory.
Dementia Care in Rural Appalachia: Multilevel Analysis of Individual- and County-Level Factors
Authors: Nah Suyoung , Savla Jyoti , Roberto Karen A
Published: April 2024

Background and Objectives

Home- and community-based services (HCBS) are underutilized, despite offering significant health benefits to both care recipients and caregivers. Drawing upon Andersen’s extended behavioral model of health services use, we examined individual- and county-level factors influencing HCBS utilization for dementia care in rural Appalachia.

Research Design and Methods

We analyzed data from telephone interviews with 123 dementia family caregivers in rural Appalachian counties (Mage = 64.7, SDage = 12.2). Multilevel analyses were conducted to examine the effects of individual-level and county-level factors on the use of home-based services (home healthcare and personal care services) as well as community-based services (adult day care and transportation services).

Results

Results indicated that caregivers’ receipt of informal support from family or friends was associated with more use of home-based services (B = 0.42, p = .003). Conversely, longer travel times to service providers were linked to use of fewer community-based services (B = −0.21, p < .001). Residing in counties with more home health agencies was associated with higher utilization of home-based services (B = 0.41, p = .046). However, higher county tax expenditures for HCBS were not linked to home-based or community-based service use.

Discussion and Implications

Findings suggest that informal support in caring for the person living with dementia enables HCBS use in rural Appalachia. In contrast, limited geographic accessibility and service availability can impede HCBS use in rural regions. Policymakers are urged to allocate direct public funding to service providers to expand service availability in underresourced rural regions.
Reliability and Responsiveness of Clinical and Endoscopic Outcome Measures in Crohn’s Disease
Authors: Khanna Reena , Feagan Brian G , Zou Guangyong , Stitt Larry W , McDonald John W D , Bressler Brian , Panaccione Remo , Shackelton Lisa M , VanViegen Tanja , Loftus Edward V , Daperno Marco , Jairath Vipul , D’Haens Geert , Sandborn William J
Published: April 2024

Background

Regulatory guidance for Crohn’s disease trials recommends coprimary efficacy end points that evaluate both symptoms and mucosal inflammation. We aimed to characterize the operating properties of commonly used disease activity assessments alone and in combination.

Methods

Endoscopic and clinical data were available for 129 participants from the Study of Biologic and Immunomodulator Naïve Patients in Crohn’s Disease trial. Readers scored the Simple Endoscopic Score for Crohn’s Disease and the Crohn’s Disease Endoscopic Index of Severity using standardized conventions. Index reliability was determined using intraclass correlation coefficients. Index responsiveness was assessed using standardized effect sizes based upon treatment assignment. Outcomes were evaluated for optimal sensitivity to treatment effect.

Results

Substantial inter-rater reliability was observed when the Simple Endoscopic Score for Crohn’s Disease and Crohn’s Disease Endoscopic Index of Severity were used as continuous measures (intraclass correlation coefficient, 0.64; 95% confidence interval [CI], 0.50-0.73; and 0.62 95% CI, 0.36-0.77) compared with moderate reliability when dichotomized (0.46; 95% CI, 0.26-0.65; and 0.51; 95% CI, 0.00-0.78). The Simple Endoscopic Score for Crohn’s Disease, Crohn’s Disease Endoscopic Index of Severity, patient-reported outcome-2, and Crohn’s Disease Activity Index were similarly responsive (standardized effect size, 0.43, 95% CI, 0.05-0.81; 0.38, 95% CI, 0.0-0.76; 0.53, 95% CI, 0.15-0.91). A composite outcome of Crohn’s Disease Activity Index score <150 and Crohn’s Disease Endoscopic Index of Severity score <6 was most sensitive to treatment effect (28.9%; 95% CI, 11.0%-46.8%; P = .003).

Conclusion

Endoscopic indices were more reliable as continuous measures. Composite outcomes including endoscopy improved sensitivity to treatment effect.
Preliminary analysis of a parabolic trough concentrating solar power system integrated with radiative cooling
Authors: Zhang Han , Hu Tianxiang , Zhao Bin , Pei Gang
Published: April 2024

Parabolic trough concentrating (PTC) solar power generation is the most technologically mature way of concentrating solar power technology. PTC plants are generally located in flat desert areas, with sufficient sunshine but lacking water for condenser cooling. Herein, a novel cooling system, radiative cooling (RC) integrated with a parabolic trough reflector, is proposed for the PTC system, which means that the waste heat generated during power generation can be radiated to the colder universe by the parabolic reflectors instead of being entirely dissipated to ambient air without water evaporation or land occupation. The simulation results demonstrate the potential of the proposed cooling system to serve as an independent cooling system by adjusting the temperature difference between radiator and ambient within −4.1 to 9.3°C, with 100% water savings and a water pump power consumption rate of 1.8–2.1%. The capital cost of implementing this new cooling system is estimated to be $27.4–54.5/kWe. Furthermore, an annual average of 86.1% of total cooling capacity is dissipated through thermal radiation, with 14.4% directly sent to the cold universe through the atmosphere window, providing a possible method to solve the water problem of power plants in torrid-arid areas and curb global warming if large-scale applications are used.
Short-term PV power prediction based on VMD-CNN-IPSO-LSSVM hybrid model
Authors: Jiang Jianjian , Hu Shizhao , Xu Liang , Wang Tianlin
Published: April 2024

This article discusses the significance and obstacles of short-term power prediction in photovoltaic systems and introduces a hybrid model for photovoltaic short-term power prediction technology based on variational mode decomposition (VMD), convolutional neural network (CNN), improved particle swarm optimization (IPSO) and least squares support vector machine (LSSVM). In the initial stage, the photovoltaic generation signal is decomposed into multiple Intrinsic mode functions (IMFs) using VMD to enhance the extraction of signal time–frequency characteristics. Subsequently, CNN is utilized for feature learning and extraction of each IMF, modeling the nonlinear and non-stationary features. Following this, the IPSO-LSSVM optimization algorithm is employed to establish and optimize multiple LSSVM models, predicting power fluctuations at different time scales. Finally, the predictions from each model are synthesized to obtain the final photovoltaic short-term power forecast. Through validation with actual photovoltaic generation data, this hybrid model demonstrates high accuracy and reliability in short-term power prediction, showing an average relative error and root mean square error reduction of 15.23 and 53.60%, respectively, compared to a certain comparative model. This proposed method based on VMD-CNN-IPSO-LSSVM hybrid model for photovoltaic power prediction holds promising prospects and practical value in the operation and scheduling of photovoltaic generation systems.
Short-term wind speed forecasting based on a hybrid model that integrates PSO-LSSVM and XGBoost
Authors: Shi Yanhua
Published: April 2024

A groundbreaking method is proposed to mitigate the impact of unpredictable fluctuations in wind velocity on wind power generation. This innovative approach integrates the particle swarm optimization (PSO)-least squares support vector machine (LSSVM) and XGBoost models in a harmonious manner. Initially, the raw wind speed data is subjected to wavelet threshold denoising to reduce noise and volatility. For short-term wind speed prediction, a PSO-LSSVM-XGBoost model is introduced. After the initial wind speed sequence undergoes wavelet threshold denoising, the enhanced sequence is forecasted using the LSSVM model, with its hyperparameters optimized through the PSO algorithm. The errors, obtained by subtracting the predicted values from the original data, are compensated using XGBoost. The final forecast results combine the rectified error data with the initial projected results. Experimental findings demonstrate the model’s remarkable capability to enhance prediction performance and accuracy.
Strong Probabilistic Stability in Holomorphic Families of Endomorphisms of ℙk (ℂ) and Polynomial-Like Maps
Authors: Bianchi Fabrizio , Rakhimov Karim
Published: April 2024

We prove that, in stable families of endomorphisms of $\mathbb{P}^{k} (\mathbb C)$, the measurable holomorphic motion of the Julia sets introduced by Berteloot, Dupont, and the first author is unbranched at almost every point with respect to all measures on the Julia set with strictly positive Lyapunov exponents and not charging the post-critical set. This provides a parallel in this setting to the probabilistic stability of Hénon maps by Berger–Dujardin–Lyubich. An analogous result holds in families of polynomial-like maps of large topological degree. In this case, we also give a sufficient condition for the positivity of the Lyapunov exponents of an ergodic measure in terms of its measure-theoretic entropy, generalizing to this setting an analogous result by de Thélin and Dupont valid on $\mathbb{P}^{k} (\mathbb C)$.
Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton
Authors: Tamayo-Leiva Javier , Alcorta Jaime , Sepúlveda Felipe , Fuentes-Alburquenque Sebastián , Arroyo José Ignacio , González-Pastor José Eduardo , Díez Beatriz
Published: April 2024

Mobile genetic elements (MGEs), collectively referred to as the “mobilome”, can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.
Collective Memory and Problems of Scale in International Relations
Authors: Sammons Elise , Kujala Will
Published: April 2024

International relations (IR) scholars are increasingly interested in the role of memory in world politics. In this paper, we examine a key tension in the uptake of memory in IR between its status as a topic studied within IR and its use as an optic through which the basic categories of IR might be rethought. Focusing on the problem of scales of analysis, central within memory studies more broadly, we suggest that while memory poses a challenge to typical scalar arrangements in IR, such as “levels” of analysis, memory is often studied within these very arrangements. We argue that this is significant because questions of scale are at times the central political problem at stake in international memory. We track this tension between topic and optic in studies of memory, national identity, and foreign policy; studies of collective trauma and sovereignty; and studies of conflict and cooperation over memory.
Simultaneous Determination of Fipronil, Permethrin, and Their Key Related Substances in a Topical Drug Product by a Single Stability-Indicating High-Performance Liquid Chromatography Method
Authors: Rathnasekara Renuka P , Tian Jingzhi , Rustum Abu M
Published: April 2024

Background

The topical veterinary drug product containing fipronil and permethrin provides an effective repellent protection and high insecticidal efficacy for dogs.

Objective

The objective of this study was to develop a stability-indicating high-performance liquid chromatography (HPLC) method for simultaneous detection and quantification of fipronil, permethrin, their key degradation products, and butylated hydroxytoluene (BHT) in a topical drug product.

Method

The two active ingredients, their degradation products, and the antioxidant (BHT) were separated by a gradient elution on a Phenomenex Kinetex C18 column (150 × 3 mm, 2.6 µm particle size) maintained at 37°C with H2O “acetonitrile “isopropyl alcohol “85% H3PO4 (65.5 + 32.5 + 4/0.0053, v/v/v/v) as mobile phase A and acetonitrile (100%) as mobile phase B. The flow rate was 0.9 mL/min, and analytes were detected and quantified at 235 nm.

Results

The specificity of the method was demonstrated by adequate separation of fipronil, permethrin, their degradation products, and BHT in the forced degraded finished product. The linearity of the method was demonstrated in the range of 0.2% to 150% of target analytical concentration of both active ingredients and 50% to 150% for BHT. Excellent recoveries of fipronil, permethrin, and BHT in placebo spiked active ingredient solutions in the linearity range showed sufficient accuracy of the method. The LOQ and LOD of the method were determined to be 0.2% and 0.07% of the analytical concentration. A robustness study did not identify any critical parameter that adversely affected the separation and quantification.

Conclusions

Here, we report the development and validation of a robust, stability-indicating HPLC method for identification and assay of fipronil, permethrin, and BHT, including estimation of fipronil’s and permethrin’s degradation products in a topical drug product for dogs.

Highlights

The new HPLC method permits the acquisition of data for all analytes of interest for a topical finished drug product containing fipronil, permethrin, and BHT.
Postmortem concentrations for total blood carbon monoxide (TBCO) as a novel biomarker for carbon monoxide (CO) poisonings
Authors: Oliverio Stefania , Ferger Marie-Caroline , Yegles Michel
Published: April 2024

Total blood carbon monoxide (TBCO) showed promising results in improving accuracy of CO determinations in blood and presenting better stability to different storage conditions. Therefore, it was proposed as an alternative biomarker to carboxyhemoglobin (COHb) for CO poisoning diagnosis. However, given that current interpretation reference values exist for COHb only, it is difficult to implement TBCO analysis in routine. Therefore, we aimed at determining TBCO reference values for postmortem CO poisoning cases. A previously validated method for TBCO analysis via gas chromatography–mass spectrometry was applied to cardiac, peripheral, cranial and spleen blood samples collected from 92 autopsies. Autopsy cases included 21 non-CO-related and 71 CO-related cases with varying postmortem intervals (PMIs). Statistical analyses were performed using statistical software R Studio. When comparing lower to higher PMIs for non-CO-related cases, no significant differences were found, which suggests that CO formation or degradation at low PMIs does not occur. Spleen blood showed potential as an alternative matrix to CO determinations in cases with sample availability issues but needs to be evaluated for CO-positive cases. Results for cardiac blood in CO-related autopsies showed a positive correlation between COHb and TBCO values (R = 0.78). This value is lower than what is found in the literature, suggesting that even though COHb and TBCO are correlated, a potential underestimation of the true CO exposure might occur if only COHb values are taken into consideration. Samples were divided into CO exposure groups based on COHb concentrations, and with the data obtained, classification into the following TBCO concentration groups is proposed: no significant CO exposure case <6 µmol/mL, medium CO exposure case 6–20 µmol/mL and high CO exposure case >20 µmol/mL. Even if a higher number of samples in each group would enable to increase the confidence, these results are very promising and highlight the importance of TBCO measurement.
South African attitudes towards refugee settlement: Examining the importance of threat perceptions
Authors: Gordon Steven Lawrence
Published: April 2024

Compared to many other countries, South Africa has quite a liberal refugee settlement policy. But public hostility towards refugees in the country is a serious obstacle to refugee protection. To understand what is driving anti-refugee sentiment amongst the masses, this study investigates refugee settlement policy preferences in the post-apartheid nation. Data from the 2020 round of the nationally representative South African Social Attitudes Survey (N = 3133) was used. Different possible drivers of policy preferences were tested. Data analysis showed that there was a robust relationship between immigrant threat perceptions and policy preferences. This finding is consistent with integrated threat theory, highlighting the damaging effects of widespread negative stereotypes about immigrants in the country. Other notable drivers of attitudes identified include economic anxiety and religiosity. Subjective knowledge, by contrast, only had a weak effect on attitude formation. The study concludes by discussing future research opportunities on anti-refugee sentiment in an African context.
A case report of a 5 mm port site hernia that occurred at the drain insertion site after laparoscopic right nephrectomy
Authors: Kawamura Yoshiaki , Uchida Takato , Umemoto Tatsuya , Nakajima Nobuyuki , Nitta Masahiro , Hasegawa Masanori , Shoji Sunao
Published: April 2024

A 5 mm port site hernia during laparoscopic surgery is rarer than a 12 mm port site hernia. Here, we report the case of a 5 mm port site hernia in an 85-year-old woman who underwent long-term steroid therapy and laparoscopic right nephrectomy. There was also a hernia at the port site where the drain was placed. Due to the 5 mm port at the drain removal site, fascial suturing was impossible after removal of the drain, and countermeasures were difficult. However, we believe that patients at a higher risk of port need suturing wound patients like this and should be carefully observed.
The Damietta Server: a comprehensive protein design toolkit
Authors: Grin Iwan , Maksymenko Kateryna , Wörtwein Tobias , ElGamacy Mohammad
Published: April 2024

The growing importance of protein design to various research disciplines motivates the development of integrative computational platforms that enhance the accessibility and interoperability of different design tools. To this end, we describe a web-based toolkit that builds on the Damietta protein design engine, which deploys a tensorized energy calculation framework. The Damietta Server seamlessly integrates different design tools, in addition to other tools such as message-passing neural networks and molecular dynamics routines, allowing the user to perform multiple operations on structural models and forward them across tools. The toolkit can be used for tasks such as core or interface design, symmetric design, mutagenic scanning, or conformational sampling, through an intuitive user interface. With the envisioned integration of more tools, the Damietta Server will provide a central resource for protein design and analysis, benefiting basic and applied biomedical research communities. The toolkit is available with no login requirement through https://damietta.de/.
Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery
Authors: Hanssen Friederike , Garcia Maxime U , Folkersen Lasse , Pedersen Anders Sune , Lescai Francesco , Jodoin Susanne , Miller Edmund , Seybold Matthias , Wacker Oskar , Smith Nicholas , Gabernet Gisela , Nahnsen Sven
Published: April 2024

DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2 emissions low. The code is available at https://nf-co.re/sarek.
Microbiome compositional data analysis for survival studies
Authors: Pujolassos Meritxell , Susín Antoni , Calle M.Luz
Published: April 2024

The growing interest in studying the relationship between the human microbiome and our health has also extended to time-to-event studies where researchers explore the connection between the microbiome and the occurrence of a specific event of interest. The analysis of microbiome obtained through high throughput sequencing techniques requires the use of specialized Compositional Data Analysis (CoDA) methods designed to accommodate its compositional nature. There is a limited availability of statistical tools for microbiome analysis that incorporate CoDA, and this is even more pronounced in the context of survival analysis. To fill this methodological gap, we present coda4microbiome for survival studies, a new methodology for the identification of microbial signatures in time-to-event studies. The algorithm implements an elastic-net penalized Cox regression model adapted to compositional covariates. We illustrate coda4microbiome algorithm for survival studies with a case study about the time to develop type 1 diabetes for non-obese diabetic mice. Our algorithm identified a bacterial signature composed of 21 genera associated with diabetes development. coda4microbiome for survival studies is integrated in the R package coda4microbiome as an extension of the existing functions for cross-sectional and longitudinal studies.
Impact of sleep disturbance in shift workers on hippocampal volume and psychomotor speed
Authors: Song Yumi , Kim Shinhye , Joo Yoonji , Ha Eunji , Shim Youngeun , Lee Hyeonji , Jeong Hyeonseok , Lyoo InKyoon , Yoon Sujung , Lee Suji
Published: April 2024

Study Objectives

Shift work interferes with circadian rhythms, affecting sleep quality and cognitive function. Poor sleep quality in shift worker (SW)s can impair psychomotor performance due to fatigue and sleepiness, increasing the risk of errors, accidents, and reduced productivity. Given the potential for atrophic changes in the hippocampus due to sleep disturbances, our study investigates how poor sleep quality correlates with hippocampal structural alterations and impacts psychomotor performance among SWs.

Methods

We recruited 100 SWs, classifying them based on sleep quality into two groups: good sleep-SW group (n = 59) and poor sleep-SW group (n = 41). Sleep quality was assessed using both 7-day actigraphy for sleep efficiency and the Pittsburgh Sleep Quality Index. A control group of 106 non-SWs without sleep problems (non-SW group) was also included for comparison. The outcome measures were psychomotor speed and hippocampal volumes, both total and by subfield.

Results

The poor sleep-SW group showed significantly smaller hippocampal volumes than both the good sleep-SW group (p < .001) and the non-SW group (p = .003). Longer shift work years correlated with greater reductions in hippocampal volume in this group (r = −0.42, p = .009), unlike in the good sleep-SW group (r = 0.08, p = .541). Furthermore, they demonstrated declines in psychomotor speed relative to the non-SW group (p = .006), which correlated with smaller hippocampal volumes (r = 0.37, p = .020).

Conclusions

SWs with poor sleep quality exhibit significant hippocampal volume reductions and psychomotor speed decline, underscoring the importance of early intervention and support for sleep issues in this population.
Water status dynamics and drought tolerance of juvenile European beech, Douglas fir and Norway spruce trees as dependent on neighborhood and nitrogen supply
Authors: Paligi Sharath S , Lichter Jens , Kotowska Martyna , Schwutke Rebecca L , Audisio Michela , Mrak Klara , Penanhoat Alice , Schuldt Bernhard , Hertel Dietrich , Leuschner Christoph
Published: April 2024

To increase the resilience of forests to drought and other hazards, foresters are increasingly planting mixed stands. This requires knowledge about the drought response of tree species in pure and mixed-culture neighborhoods. In addition, drought frequently interacts with continued atmospheric nitrogen (N) deposition. To disentangle these factors for European beech, Norway spruce and Douglas fir, we conducted a replicated 3-factorial sapling growth experiment with three moisture levels, (high, medium, and low), two N levels (high and ambient), and pure and mixed-culture neighborhoods. We measured biomass, stomatal conductance (GS), shoot water potential (at predawn: ΨPD, midday, and turgor loss point: ΨTLP), branch xylem embolism resistance (Ψ50) and minimum epidermal conductance (Gmin). The three species differed most with respect to Gmin (10-fold higher in beech than in the conifers), hydroscape area (larger in beech), and the time elapsed to reach stomatal closure (TΨGS90) and ΨTLP (TTLP; shorter in beech), while Ψ50 and ΨTLP were remarkably similar. Neighborhood (pure vs mixed-culture) influenced biomass production, water status and hydraulic traits, notably GS (higher in Douglas fir, but lower in spruce and beech, in mixtures than pure culture), hydraulic safety margin (smaller for beech in mixtures), and TΨGS90 and TTLP (shorter for spruce in mixture). High N generally increased GS, but no consistent N effects on leaf water status and hydraulic traits were detected, suggesting that neighbor identity had a larger effect on plant water relations than N availability. We conclude that both tree neighborhood and N availability modulate the drought response of beech, spruce, and Douglas fir. Species mixing can alleviate the drought stress of some species, but often by disadvantaging other species. Thus, our study suggests that stabilizing and building resilience of production forests against a drier and warmer climate may depend primarily on the right species choice; species mixing can support the agenda.
Mental health implications and psychologic factors in workers' compensation cases
Authors: Brown Kristi
Published: April 2024

Work-related injuries can harm mental health and affect other facets of injured workers' lives. Clinicians must be aware of the problem of emotional distress and treat the whole patient after a workplace injury. More education and information are needed for clinicians, employers, and workers' compensation carriers so that injured workers can be properly screened for mental health issues and supported during treatment. Further research is needed to establish a protocol for early intervention to minimize the negative emotional and mental health effects of workplace injuries.
State Abortion Bans Heap Burdens on Already Traumatized Rape Survivors
Authors: Roush Karen
Published: April 2024

The laws exacerbate stigma and impede access to needed health care.
Navigating Clinical Questions
Authors: Graham Debra Barrett
Published: April 2024

Lead with the problem, never the intervention.
Virtual Reality an Option for PPE Skills Training
Authors: Rosenberg Karen
Published: April 2024

According to this study:
Regenerative Medicine in Gynecology
Authors: Balough Julia L. , Moalli Pamela
Published: April 2024

The female reproductive tract undergoes dynamic changes across the life span. Congenital abnormalities, life events, and medical interventions can negatively affect the structure and function of reproductive tract organs, resulting in lifelong sequelae. The objective of regenerative gynecology is to discover and promote endogenous mechanisms by which a healthy tissue maintains overall tissue integrity after injury, after disease, or with age. In this review, we discuss some of the key state-of-the-art cell-based and scaffolding therapies that have been applied to regenerate gynecologic tissues and organs primarily in animal and tissue culture models. We further discuss the limitations of current technologies, problems of implementation and scalability, and future outlook of the field.
Dermoscopic-Guided Shave Removal of Acquired Facial Melanocytic Nevi in Dark-Skinned Individuals
Authors: Rezk Ahmed Fawzy , Touni Ahmed Ahmed
Published: April 2024

BACKGROUND

Acquired melanocytic nevi are common benign skin lesions that require removal under certain circumstances. Shave removal is a straightforward treatment modality with a risk of recurrence.

OBJECTIVE

To evaluate the outcome of dermoscopy-guided shave removal of acquired melanocytic nevi in the face of dark-skinned individuals who are more liable to postsurgical complications.

METHODS

The study was conducted on 64 patients with acquired facial melanocytic nevi. Serial shave removal using a razor blade guided by dermoscopic examination was done until nevus-free tissue was seen, followed by electrocauterization of the base. Cosmetic outcome, patients' satisfaction, and recurrence rate were evaluated during follow-up.

RESULTS

Excellent cosmetic outcome was achieved in 54.69% of patients, while 39.06% had an acceptable outcome, and 6.25% of patients had poor cosmetic outcome. Meanwhile, the recurrence rate was noticed in 5 cases only (7.8%).

CONCLUSION

Dermoscopic-guided shave removal provides an easy procedure of treating common melanocytic nevi with an acceptable cosmetic result and a lower rate of recurrence even in patients with darker skin phenotypes.
HPV Vaccination Practices Among Medical Trainees in Pediatrics, Obstetrics and Gynecology, and Family Medicine
Authors: Cagle-Colon Kayla J. , Voigt Paxton , Boyd Leslie
Published: April 2024

Objective

The human papillomavirus (HPV) vaccine has been proven effective in preventing HPV-related cancer. However, vaccination uptake in the United States remains unacceptably low. The aim of this study is to determine whether residents' HPV vaccination status, demographics, or residency training setting are predictive of vaccination prescribing practices.

Methods

This was an anonymous, IRB-approved, opt-in survey of OBGYN, Family Medicine, and Pediatric residents. Using the National Residency Match Program Web site, surveys were sent to program directors requesting their residents' participation. Demographics, practice settings, HPV vaccination status, reasons for being inappropriately vaccinated, and resident vaccination-prescribing practices were analyzed.

Results

A total of 853 residents participated. A total of 56.7% of respondents were fully vaccinated against HPV. The most common reasons for being unvaccinated were as follows: age (51.7%, n = 122), monogamous (30.9%, n = 73), do not believe it works (22.5%, n = 53), and affordability/insurance did not cover (14.4%, n = 34). Residents working in an urban setting were more likely to be vaccinated than those in suburban (odds ratio [OR] = 1.93, 95% confidence interval [CI], 1.364–3.229, p < .001) or rural (OR = 2.08, 95% CI 1.461–3.359, p 0.01) settings. Males were less likely than females (OR = 0.90, 95% CI 0.702–0.997, p < .001) to be vaccinated. Single residents were more likely to be vaccinated than married (OR = 2.56, 95% CI 2.444–2.704, p < .001) or divorced (OR = 2.15, 95% CI 1.822–3.264, p 0.21) residents. Vaccinated residents were more likely to recommend HPV vaccination to their patients than those who were unvaccinated (OR = 1.83, 95% CI 1.321–2.548, p .004).

Conclusions

A significant portion of Family Medicine, Pediatrics, and OBGYN residents have not received appropriate vaccination against HPV. Vaccination is highest among residents who identify as female, single, or working in urban settings. Vaccinated residents were also found to be almost 2 times as likely to recommend vaccination to their patients. As such, our data suggest that targeted provider education is needed to increase vaccination rates for both trainees and their patients.
Commonly Drawn Immunologic and Inflammatory Markers as Risk Predictors for Anal Cancer in Veterans Living With HIV
Authors: Stem Jonathan , Hewitt Austin J. , Yang Qiuyu , Sanger Cristina B.
Published: April 2024

Objectives

This study aimed to determine if immune inflammatory markers (neutrophil lymphocyte ratio [NLR], platelet lymphocyte ratio [PLR], and prognostic nutritional index [PNI]) correlate with anal cancer risk in people living with HIV and to compare these markers with the CD4/CD8 ratio.

Materials and Methods

This is a regional retrospective cohort study of veterans living with HIV who were screened for or diagnosed with anal neoplasia or cancer from 2001 to 2019. The NLR, PLR, PNI, and CD4/CD8 ratio within 1 year of anal pathology results were computed. Patients with anal cancer were compared to patients without anal cancer. Regression modeling was used to estimate the odds of developing anal cancer.

Results

Three hundred thirty-four patients were included (37 with anal cancer, 297 without anal cancer). In patients with anal cancer, NLR and PLR were higher (2.17 vs 1.69, p = .04; 140 vs 110, p = .02, respectively), while PNI and CD4/CD8 ratio were lower (44.65 vs 50.01, p < .001; 0.35 vs 0.80, p < .001, respectively). On multivariate logistic regression modeling, only PNI (odds ratio, 0.90; p = .001) and CD4/CD8 ratio (odds ratio, 0.05; p < .001) were associated with increased anal cancer risk.

Conclusions

Although NLR and PLR independently correlate with anal cancer risk, when controlling for other risk predictors, only PNI and CD4/CD8 ratio were statistically significant biomarkers for anal cancer. The CD4/CD8 ratio is the strongest immune inflammatory marker that predicts risk of anal cancer among veterans living with HIV.
Inability to belch syndrome: what the gastroenterologist needs to know
Authors: Smout André , Bredenoord Albert J. , Oude Nijhuis Renske
Published: April 2024

Purpose of review

To review recent publications on the inability to belch syndrome.

Recent findings

Five recent retrospective case series indicate that the inability to belch syndrome usually starts in early childhood and is often accompanied by gurgling noises in the chest, pain in the chest or upper abdomen, bloating, and excessive flatulence. Currently, the vast majority of patients who have been identified with inability to belch have self-diagnosed the syndrome on the basis of information available on the internet. A favorable response to injection of botulinum toxin in the cricopharyngeus muscle is regarded as confirmation of the diagnosis. In a mechanistic study in eight patients, absence of reflexogenic relaxation of the upper esophageal sphincter upon rapid gaseous esophageal distension was confirmed to play a pivotal role in the pathogenesis of the syndrome.

The inability to belch syndrome, caused by failure of the upper esophageal sphincter to relax when the esophageal body is distended, clearly exists and may not be as rare as thought hitherto. However, overdiagnosis is also likely to occur because the diagnosis is usually made on the basis of symptoms only. The efficacy of botulinum toxin injection in the upper sphincter needs to be assessed in double-blind placebo-controlled studies.
Endoscopic ultrasound-guided radiofrequency ablation of pancreatic tumors
Authors: Patel Vanisha , Abdelbaki Ahmed , Thosani Nirav C. , Krishna Somashekar G.
Published: April 2024

Purpose of review

Surgery is a cornerstone in the management of pancreatic cancer and precancerous pancreatic lesions. However, many patients are not suitable candidates for surgery at the time of diagnosis for various reasons. Endoscopic ultrasound-guided radiofrequency ablation (EUS-RFA) appears to be a promising treatment option for patients who are ineligible for surgery for management of pancreatic adenocarcinoma (PDAC), and pancreatic neuroendocrine tumors (PNETs), and pancreatic cystic lesions (PCLs).

Recent findings

EUS-RFA may serve as an adjunct to chemotherapy or palliative measures for inoperable cases of PDAC. Given its feasibility and efficacy, EUS-RFA has an evolving niche as a minimally invasive and potentially definitive treatment for PNETs and high-risk PCLs such as intraductal papillary mucinous neoplasms (IPMNs). EUS-RFA is a generally well tolerated procedure, with abdominal pain and acute pancreatitis being the most common adverse effects, though the risk can be mitigated through prophylactic measures.

There is an increasing body of evidence to support the use of EUS-RFA in managing pancreatic lesions, either as definitive, adjunctive, or palliative treatment, depending on lesion type.