bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional and translational dynamics underlying heat shock response in the thermophilic crenarchaeon
Sulfolobus acidocaldarius
Authors: Baes Rani , Grünberger Felix , Pyr dit Ruys Sébastien , Couturier Mohea , De Keulenaer Sarah , Skevin Sonja , Van Nieuwerburgh Filip , Vertommen Didier , Grohmann Dina , Ferreira-Cerca Sébastien , Peeters Eveline 
Published: August 2023

ABSTRACT

High-temperature stress is critical for all organisms and induces a profound cellular response. For Crenarchaeota, little information is available on how heat shock affects cellular processes and on how this response is regulated. We set out to study heat shock response in the thermoacidophilic model crenarchaeon
Sulfolobus acidocaldarius,
which thrives in volcanic hot springs and has an optimal growth temperature of 75°C. Pulse-labeling experiments demonstrated that a temperature shift to 86°C induces a drastic reduction of the transcriptional and translational activity, but that RNA and protein neosynthesis still occurs. By combining RNA sequencing and mass spectrometry, an integrated mapping of the transcriptome and proteome was performed. This revealed that heat shock causes an immediate change in the gene expression profile, with RNA levels of half of the genes being affected, followed by a more subtle reprogramming of the protein landscape. Functional enrichment analysis indicated that nearly all cellular processes are affected by heat shock. A limited correlation was observed in the differential expression on the RNA and protein level, suggesting a prevalence of post-transcriptional and post-translational regulation. Furthermore, promoter sequence analysis of heat shock regulon genes demonstrated the conservation of strong transcription initiation elements for highly induced genes, but an absence of a conserved protein-binding motif. It is, therefore, hypothesized that histone-lacking archaea such as Sulfolobales use an evolutionarily ancient regulatory mechanism that relies on temperature-responsive changes in DNA organization and compaction induced by the action of nucleoid-associated proteins, as well as on enhanced recruitment of initiation factors.

IMPORTANCE

Heat shock response is the ability to respond adequately to sudden temperature increases that could be harmful for cellular survival and fitness. It is crucial for microorganisms living in volcanic hot springs that are characterized by high temperatures and large temperature fluctuations. In this study, we investigated how
S. acidocaldarius
, which grows optimally at 75°C, responds to heat shock by altering its gene expression and protein production processes. We shed light on which cellular processes are affected by heat shock and propose a hypothesis on underlying regulatory mechanisms. This work is not only relevant for the organism’s lifestyle, but also with regard to its evolutionary status. Indeed,
S. acidocaldarius
belongs to the archaea, an ancient group of microbes that is more closely related to eukaryotes than to bacteria. Our study thus also contributes to a better understanding of the early evolution of heat shock response.
Patient preferences for stress urinary incontinence treatments: a discrete choice experiment
Authors: Boyers Dwayne , Kilonzo Mary , Davidson Tracey , Cooper David , Wardle Judith , Bhal Kiron , N'Dow James , MacLennan Graeme , Norrie John , Abdel-Fattah Mohamed 
Published: August 2023

ObjectivesTo elicit and value patient preferences for the processes and outcomes of surgical management of stress urinary incontinence in women.DesignA discrete choice experiment survey to elicit preferences for type of anaesthesia, postoperative recovery time, treatment success, adverse events, impact on daily activities and cost. An experimental design generated 40 choice tasks, and each respondent completed 1 block of 10 and 2 validity tests. Analysis was by multinomial logistical regression.SettingN=21 UK hospitals.ParticipantsN=325 adult women who were a subsample of those randomised to the single-incision mini-slings clinical trial.OutcomesPatient preferences; valuation obtained using willingness to pay.ResultsN=227 of 325 (70%) returned a questionnaire, and 94% of those completed all choice tasks. Respondents preferred general anaesthesia, shorter recovery times, improved stress urinary incontinence symptoms and avoidance of adverse events. Women were willing to pay (mean (95% CI)) £76 (£33 to £119) per day of reduction in recovery time following surgery. They valued increases in Patient Global Impression of Improvement, ranging from £8173 (£5459 to £10 887) for ‘improved’ to £11 706 (£8267 to £15 144) for ‘very much improved’ symptoms, compared with no symptom improvement. This was offset by negative values attached to the avoidance of complications ranging between £−8022 (£−10 661 to £−5383) and £−10 632 (£−14 077 to £−7187) compared to no complications. Women valued treatments that reduced the need to avoid daily activities, with willingness to pay ranging from £−967 (£−2199 to £266) for rarely avoiding activities to £−5338 (£−7258 to £−3417) for frequently avoiding daily activities compared with no avoidance.ConclusionThis discrete choice experiment demonstrates that patients place considerable value on improvement in stress urinary incontinence symptoms and avoidance of treatment complications. Trade-offs between symptom improvement and adverse event risk should be considered within shared decision-making. The willingness to pay values from this study can be used in future cost–benefit analyses.Trial registration numberISRCTN: 93264234; Post-results.
Identification of factors associated with non-adherence to recommended COVID-19 preventive behaviours: a cross-sectional study based on a survey among 1004 French primary care professionals
Authors: Bouton Céline , Meziere Pauline , Gaultier Aurelie , Dupouy Julie , Rat Cédric 
Published: August 2023

ObjectivesSince the beginning of the COVID-19 pandemic, adherence to preventive behaviours to limit virus spread has been a major issue. The study objective was to identify factors associated with non-adherence to preventive behaviours among general practitioners (GPs) during the COVID-19 pandemic using data from a questionnaire completed during the French National Congress of General Medicine in June 2021.DesignThis descriptive study relied on data collected with a questionnaire during the national congress on general medicine in Bordeaux, France, from 16–18 June 2021.SettingThe study was conducted in primary care in France.ParticipantsOut of a total of 1004 GPs and GP trainees, 755 completed the questionnaire during conferences and 249 were contacted by mail.ResultsThe questionnaire included questions on sociodemographic characteristics and COVID-19 related preventive behaviours, beliefs and experiences. Answers to questions that explored the Health Belief Model components were selected and then compared among participants who reported appropriate preventive behaviours (wearing face masks and social distancing) and participants who reported non-adherence. Analysis was based on multivariate logistic regression.The responders’ mean age was 35.8 years; 61.64% were women, 61.9% were practising GPs and 37.2% were GP trainees. Moreover, 96.6% of participants had completed the COVID-19 vaccination schedule. Non-adherence (reported by 72/1004 participants) was more frequent among smokers (OR=2.57, 95% CI 1.29 to 4.83, p=0.005) and younger participants (OR=0.95, 95% CI 0.92 to 0.98, p=0.005). Complete COVID-19 vaccination or a previous infection was not associated with non-adherence and has been poorly described.ConclusionMore studies are needed to confirm the factors involved in the adoption of COVID-19 preventive behaviours by healthcare professionals and to explore the beliefs and barriers to the adoption of these behaviours.
CT perfusion to measure venous outflow in acute ischemic stroke in patients with a large vessel occlusion
Authors: Adusumilli Gautam , Christensen Soren , Yuen Nicole , Mlynash Michael , Faizy Tobias D , Albers Gregory W , Lansberg Maarten G , Fiehler Jens , Heit Jeremy J 
Published: August 2023

BackgroundRobust venous outflow (VO) profiles, measured by degree of venous opacification on pre-thrombectomy CT angiography (CTA) studies, are strongly correlated with favorable outcomes in patients with large vessel occlusion acute ischemic stroke treated by thrombectomy. However, VO measurements are laborious and require neuroimaging expertise.ObjectiveTo develop a semi-automated method to measure VO using CTA and CT perfusion imaging studies.MethodsWe developed a graphical interface usingThe Visualization Toolkit,allowing for voxel selection at the confluence and bilateral internal cerebral veins on CTA along with arterial input functions (AIFs) from both internal carotid arteries. We extracted concentration–time curves from the CT perfusion study at the corresponding locations associated with AIF and venous output function (VOF). Outcome analyses were primarily conducted by the Mann-Whitney U and Jonckheere-Terpstra tests.ResultsSegmentation at the pre-selected AIF and VOF locations was performed on a sample of 97 patients. 65 patients had favorable VO (VO+) and 32 patients had unfavorable VO (VO−). VO+ patients were found to have a significantly shorter VOF time to peak (8.26; 95% CI 7.07 to 10.34) than VO− patients (9.44; 95% CI 8.61 to 10.91), P=0.007. No significant difference was found in VOF curve width and the difference in time between AIF and VOF peaks.ConclusionsTime to peak of VOF at the confluence of sinuses was significantly associated with manually scored venous outflow. Further studies should aim to understand better the association between arterial inflow and venous outflow, and capture quantitative metrics of venous outflow at other locations.
Oblique Axis Rib Stretch and Curved Planar Reformats in Patients for Rib Fracture Detection and Characterization: Feasibility and Clinical Application
Authors: Ye Jingzhi , Li Hongyi , Zhang Meng , Lin Fenghuan , Liu Jingfeng , Chen Jun , Peng Ye , Xiao Mengqiang 
Published: August 2023

Objective. To assess the use of CT with oblique axis rib stretch (OARS) and curved planar reformats (CPRs) for rib fracture detection and characterization. Methods. A total of 108 forensically diagnosed patients with rib fractures were evaluated retrospectively. OARS and CPRs were independently used during the diagnosis in two groups. In each group, the final diagnosis was made after a junior radiologist’s initial diagnosis was reviewed by a senior radiologist. The images were evaluated for the presence and characterization of rib fractures. Results. A total of 2,592 ribs were analyzed, and 326 fractured ribs and 345 fracture sites were diagnosed using reference standard. Two groups of radiologists identified 331 and 333 fracture sites using the OARS method, 291 and 288 fracture sites using the CPRs method, and 274 fracture sites in forensically diagnosed patients (CR: conventional reconstruction), respectively; and all missed diagnoses were nondisplaced rib fractures. The ROC Az value of OARS1,2 was 0.98, which is higher than CPRs1,2 0.91, and CR 0.90 (all

p

< 0.01). The Az value for detecting rib fractures using CPRs1,2 and CR has no statistical difference (

p

= 0.14 and 0.29). More misdiagnosed patients were found using CPRs1,2 (42 and 44 cases) than OARS1,2 (1 and 2 cases) and CR (2 cases). The displaced fracture detection ratio of all methods showed no difference. Conclusions. Doctors using the OARS method could improve diagnostic performance for detecting rib fractures without the requirement of specialized software and workstation when compared with CPRs.
Evaluation of Wound-Healing Activity of Hydrogel Extract of Sansevieria trifasciata Leaves (Asparagaceae)
Authors: Yuniarsih Nia , Hidayah Himyatul , Gunarti Neni Sri , Kusumawati Anggun Hari , Farhamzah Farhamzah , Sadino Asman , Alkandahri Maulana Yusuf 
Published: August 2023

For centuries, communities have used medicinal plants to treat various diseases, such as Sansevieria trifasciata (Asparagaceae), for wound healing. However, a study on the wound-healing activity of this plant has not been conducted. Therefore, this study aimed to evaluate the hydrogel formulations of S. trifasciata extract (HESt) and its activity in wound healing. The HESt formulations were subjected to physical examination, pH measurement, spreading coefficient, rheological study, stability test, and wound-healing activity. Furthermore, the HPMC and carbopol 940 gel-forming agents were used to obtain this formulation. In the incision wound model, the experiment was divided into 5 groups, each consisting of 4 mice. Groups 1 and 2 served as a negative and positive control (octenidine gel), while 3, 4, and 5 were given HESt formulations of 15%, 20%, and 25% (w/w), respectively, for 15 days. Based on the wound healing activity test, HESt 20% and 25% (w/w) groups showed significant (

p

< 0.05) wound closure area on day 4 and from day 2 to 16. However, the HESt 15% (w/w) group showed no significant difference in wound-healing activity but had a higher closure than the negative control. Based on the evaluation of the hydrogel, all HESt formulations were reported to have fulfilled the standard requirements. The HESt formulations were also reported to be stable at various temperatures in the stability test. Therefore, S. trifasciata leaves extract has the potential to be developed as a wound-healing drug derived from herbal plants formulated into hydrogel preparations.
Assessing the Genomic Landscape of Cervical Cancers: Clinical Opportunities and Therapeutic Targets
Authors: Friedman Claire F. , Ravichandran Vignesh , Miller Kathryn , Vanderbilt Chad , Zhou Qin , Iasonos Alexia , Vivek Malavika , Mishra Pamela , Leitao Mario M. , Broach Vance , Sonoda Yukio , Kyi Chrisann , Zamarin Dmitriy , O'Cearbhaill Roisin E. , Konner Jason , Berger Michael F. , Weigelt Britta , Momeni Boroujeni Amir , Park Kay J. , Aghajanian Carol , Solit David B. , Donoghue Mark T.A. 
Published: August 2023

Abstract

Purpose:
Tumor genomic profiling is increasingly used to guide treatment strategy in patients with cancer. We integrated tumor genomic, clinical demographic, and treatment response data to assess how prospective tumor-normal sequencing impacted treatment selection in patients with cervical cancer.

Experimental Design:
Cervical cancers were prospectively analyzed using the MSK-IMPACT (Memorial Sloan Kettering Cancer Center – Integrated Mutation Profiling of Actionable Cancer Targets) next-generation sequencing panel. Clinical data, including histology, stage at diagnosis, treatment history, clinical trial enrollment and outcomes, date of last follow-up, and survival status were obtained from medical records.

Results:
A total of 177 patients with cervical cancer (squamous, 69; endocervical adenocarcinoma, 50; gastric type, 22; adenosquamous, 21; and other, 15) underwent MSK-IMPACT testing. The most prevalent genomic alterations were somatic mutations or amplifications in PIK3CA (25%), ERBB2 (12%), KMT2C (10%), and KMT2D (9%). Furthermore, 13% of patients had high tumor mutational burden (TMB &gt;10 mut/Mb), 3 of which were also microsatellite instability–high (MSI-H). Thirty-seven percent of cases had at least one potentially actionable alteration designated as a level 3B mutational event according to the FDA-recognized OncoKB tumor mutation database and treatment classification system. A total of 30 patients (17%) were enrolled on a therapeutic clinical trial, including 18 (10%) who were matched with a study based on their MSK-IMPACT results. Twenty patients (11%) participated in an immune checkpoint inhibition study for metastatic disease; 2 remain progression free at &gt;5 years follow-up.

Conclusions:
Tumor genomic profiling can facilitate the selection of targeted/immunotherapies, as well as clinical trial enrollment, for patients with cervical cancer.
Climate & Language: An Entangled Crisis
Authors: Fine Julia C. , Love-Nichols Jessica , Perley Bernard C. 
Published: August 2023

Abstract
Rising ocean levels threaten entire communities with relocation. The continued erosion of Arctic coastlines due to melting ice sheets and thawing permafrost has forced Inuit communities to move to more secure locations. Each move dislodges Indigenous peoples and their languages from ancestral landscapes and ways of knowing, obligating communities to adopt colonial or majority languages. Scholars and activists have documented the intersections of climate change and language endangerment, with special focus paid to their compounding consequences. We consider the relationship between language and environmental ideologies, synthesizing previous research on how metaphors and communicative norms in Indigenous and colonial languages and cultures influence environmental beliefs and actions. We note that these academic discourses-as well as similar discourses in nonprofit and policy-making spheres-rightly acknowledge the importance of Indigenous thought to environmental and climate action. Sadly, they often fall short of acknowledging both the colonial drivers of Indigenous language “loss” and Indigenous ownership of Indigenous language and environmental knowledge. We propose alternative framings that emphasize colonial responsibility and Indigenous sovereignty. Finally, we reflect on emergent vitalities and radical hope in Indigenous language movements and climate justice movements.
Language on Trial
Authors: King Sharese , Rickford John R. 
Published: August 2023

Abstract
This essay draws on the case study we conducted of Rachel Jeantel's testimony in the 2013 trial of George Zimmerman v. The State of Florida.1 Although Jeantel, a close friend of Trayvon Martin, was an ear-witness (by cell phone) to all but the final minutes of Zimmerman's interaction with Trayvon, and testified for nearly six hours about it, her testimony was disregarded in jury deliberations. Through a linguistic analysis of Jeantel's speech, comments from a juror, and a broader contextualization of stigmatized speech forms and linguistic styles, we argue that the lack of acknowledgment of dialectal variation has harmful social and legal consequences for speakers of stigmatized dialects. Such consequences include limits on criminal justice, employment, and fair access to housing, as well as accessible and culturally sensitive education. We propose new calls to action, which include the ongoing work the coauthors are doing to address such harms, while also moving to inspire concerned citizens to act.
A Moving-Wave Implementation in WRF to Study the Impact of Surface Water Waves on the Atmospheric Boundary Layer
Authors: Zhu Peiyun , Li Tianyi , Mirocha Jeffrey D. , Arthur Robert S. , Wu Zhao , Fringer Oliver B. 
Published: August 2023

Abstract
While numerous modeling studies have focused on the interaction of ocean surface waves with the atmospheric boundary layer, most employ idealized waves that are either monochromatic or synthetically generated from a theoretical wave spectrum, and the atmospheric solvers are typically incompressible. To study wind–wave coupling in real-world scenarios, a model that can simulate both realistic meteorological and wave conditions is necessary. In this paper we describe the implementation of a moving bottom boundary condition into the Weather Research and Forecasting Model for large-eddy simulation applications. We first describe the moving bottom boundary conditions within WRF’s pressure-based vertical coordinate system. We then validate our code with idealized test cases that have analytical solutions, including flow over a monochromatic wave with and without viscosity. Finally, we present results from turbulent flows over a moving monochromatic wave with different wave ages, and demonstrate satisfactory agreement of the wave growth rate with results from the literature. We also compare atmospheric stress and wind parameters from two physically equivalent cases. The first specifies a wind moving in the same direction as a propagating wave, while the second involves a stationary wave with the wind adjusted such that the wind relative to the wave is the same as in the first case. Results indicate that the velocity and Reynolds stress profiles for the two cases match, further validating the moving bottom implementation.
Stratified Sampling: Some Associated Problems
Authors: Mukherjee S. P. 
Published: August 2023

Stratified sampling has been commonly used in many large-scale surveys. The two inter-related problems of determining strata boundaries where strata have to be developed using some variable(s) whose values can be accessed while designing the survey and of allocating the total sample size among the strata have been studied during a long period, initially without involving mathematical programming and subsequently using concurrent developments in constrained optimization methods and algorithms. The present article provides a critique of some of these studies, especially those dealing with multiple stratification variables and multiple parameters to be estimated.AMS Subject Classification: 62D05
Need for Policy Reforms in the Aftermath of COVID-19? An Analysis of Indian Pharmaceutical Sector
Authors: Banik Nilanjan , Chakraborty Debashis , Dash Sampada Kumar 
Published: August 2023

Acknowledging coronavirus disease 2019 (COVID-19) as a persistent health challenge in the foreseeable future, there is a need to evaluate how India can emerge as a major exporter in this category. This analysis with 41 COVID-19-related pharmaceutical products indicates that India currently lacks comparative advantage in several categories, for example, active pharmaceutical ingredient, medical equipment and devices, disinfectants and sterilisation products, and personal protective equipment. The country, however, enjoys a comparative advantage in manufacturing vaccines and formulations. Interestingly, India imposes higher tariffs and non-tariff measures (NTMs) on both sets of products, irrespective of the comparative advantages. Additionally, the article identifies important operational, logistic, and financial issues that can improve the efficiency of the pharmaceutical supply chain (PSC), which in turn can ensure smoother availability of these pharmaceutical products in the domestic market. While the operational issues underline the need for better coordination between multiple stakeholders, the logistic bottlenecks call for a general improvement at the infrastructure level. The financial issues correspond to infrastructural bottlenecks, transport costs and resulting cost escalation. The article concludes that the policymakers need to focus on the reduction of import barriers and improve the PSC to ensure the easier availability of COVID-19 medicines, vaccines, and related products. JEL Codes: F13, F15, I18, O25