bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synchrotron emitting Komissarov torus with magnetic polarization around Kerr black holes
Authors: Velásquez-Cadavid J M , Lora-Clavijo Fabio D , Pimentel Oscar M , Arrieta-Villamizar J A 
Published: November 2022

ABSTRACT
Magnetic fields in black hole accretion discs are associated with processes of mass accretion and energy amplification. The contribution of the magnetic field due to the magnetic polarization of the material induces effects on the physical properties of the medium that have repercussions on the radiation coming from the accretion discs. Hence, from observations, it could be possible to infer the ‘fingerprint’ left by the magnetic polarization of the material and establish the properties of the space–time itself. As the first step in this purpose, we use numerical simulations to systematically analyse the possible observable effects produced by the magnetic properties of an accretion disc around a Kerr black hole. We found that under the synchrotron radiation power-law model the effects of the magnetic polarization are negligible when the plasma is gas pressure-dominated. Nevertheless, as beta-plasma decreases, the emission becomes more intense for magnetic pressure-dominated discs. In particular, we found that paramagnetic discs emit the highest intensity value independent of the beta-plasma parameter in this regime. By contrast, the emitted flux decreases with the increase of beta-plasma due to the dependence of the magnetic field on the emission and absorption coefficients. Moreover, the disc morphology changes with the magnetic susceptibility: Paramagnetic discs are more compact than diamagnetic ones. This fact leads to diamagnetic discs emitting a greater flux because each photon has a more optical path to travel inside the disc.
TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization
Authors: Wang Xueying , Chen Lingxi , Liu Wei , Zhang Yuanzheng , Liu Dawei , Zhou Chenxin , Shi Shuai , Dong Jiajie , Lai Zhengtao , Zhao Bingran , Zhang Wenjingyu , Cheng Haoyue , Li Shuaicheng 
Published: November 2022

Abstract
Deciphering the cell-type composition in the tumor immune microenvironment (TIME) can significantly increase the efficacy of cancer treatment and improve the prognosis of cancer. Such a task has benefited from microarrays and RNA sequencing technologies, which have been widely adopted in cancer studies, resulting in extensive expression profiles with clinical phenotypes across multiple cancers. Current state-of-the-art tools can infer cell-type composition from bulk expression profiles, providing the possibility of investigating the inter-heterogeneity and intra-heterogeneity of TIME across cancer types. Much can be gained from these tools in conjunction with a well-curated database of TIME cell-type composition data, accompanied by the corresponding clinical information. However, currently available databases fall short in data volume, multi-platform dataset integration, and tool integration. In this work, we introduce TIMEDB (https://timedb.deepomics.org), an online database for human tumor immune microenvironment cell-type composition estimated from bulk expression profiles. TIMEDB stores manually curated expression profiles, cell-type composition profiles, and the corresponding clinical information of a total of 39,706 samples from 546 datasets across 43 cancer types. TIMEDB comes readily equipped with online tools for automatic analysis and interactive visualization, and aims to serve the community as a convenient tool for investigating the human tumor microenvironment.
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
Authors: Terlouw Barbara R , Blin Kai , Navarro-Muñoz Jorge C , Avalon Nicole E , Chevrette Marc G , Egbert Susan , Lee Sanghoon , Meijer David , Recchia Michael J J , Reitz Zachary L , van Santen Jeffrey A , Selem-Mojica Nelly , Tørring Thomas , Zaroubi Liana , Alanjary Mohammad , Aleti Gajender , Aguilar César , Al-Salihi Suhad A A , Augustijn Hannah E , Avelar-Rivas J Abraham , Avitia-Domínguez Luis A , Barona-Gómez Francisco , Bernaldo-Agüero Jordan , Bielinski Vincent A , Biermann Friederike , Booth Thomas J , Carrion Bravo Victor J , Castelo-Branco Raquel , Chagas Fernanda O , Cruz-Morales Pablo , Du Chao , Duncan Katherine R , Gavriilidou Athina , Gayrard Damien , Gutiérrez-García Karina , Haslinger Kristina , Helfrich Eric J N , van der Hooft Justin J J , Jati Afif P , Kalkreuter Edward , Kalyvas Nikolaos , Kang Kyo Bin , Kautsar Satria , Kim Wonyong , Kunjapur Aditya M , Li Yong-Xin , Lin Geng-Min , Loureiro Catarina , Louwen Joris J R , Louwen Nico L L , Lund George , Parra Jonathan , Philmus Benjamin , Pourmohsenin Bita , Pronk Lotte J U , Rego Adriana , Rex Devasahayam Arokia Balaya , Robinson Serina , Rosas-Becerra L Rodrigo , Roxborough Eve T , Schorn Michelle A , Scobie Darren J , Singh Kumar Saurabh , Sokolova Nika , Tang Xiaoyu , Udwary Daniel , Vigneshwari Aruna , Vind Kristiina , Vromans Sophie P J M , Waschulin Valentin , Williams Sam E , Winter Jaclyn M , Witte Thomas E , Xie Huali , Yang Dong , Yu Jingwei , Zdouc Mitja , Zhong Zheng , Collemare Jérôme , Linington Roger G , Weber Tilmann , Medema Marnix H 
Published: November 2022

Abstract
With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.
Bird signs can be important for ecocultural conservation by highlighting key information networks in people–bird communities
Authors: Wyndham Felice S , Park Karen E 
Published: November 2022

AbstractThe ways people think, feel, speak about, and act in and with environments are inextricably intertwined with the well-being of other living things, including birds. We report on the kinds of messages contained in 598 examples of locally-defined signs from 498 bird taxa from 169 sources and 123 ethnolinguistic groups. Using Peirce’s three sign forms: symbolic, iconic, and indexical, we analyze one aspect of human–bird interactions: that of reading bird sign for ecological and social interpretations. Understanding ecological semiotic nuance is important for translating between local, regional, and global science, and for respecting autonomous processes of local people attributing value or lack thereof to birds and their habitats. Over one-third of the signs in our sample (216; 36%) were specifically described as omens of some kind, commonly of death, illness, or something “bad”. Three modes of message delivery account for the majority of the data: predicting (60%), bringing (15%; including news, rain, luck), and indicating (15%; including seasonal change, fruit ripening, animals). Reading birds to predict weather (especially rain) was common, as was listening to and interpreting birds’ alarm calls warning of snakes or predators, and knowing that a certain bird indicates the presence of certain other animals, or of a water source. We collected 51 examples of warblish, the imitation or translation of bird sounds into non-onomatopoeic words. We argue for the amplification of ecocultural conservation (attending to histories of human–nonhuman relationships in place) to channel resources and land control to local and Indigenous managers who are immersed in relevant bird–people information networks. We discuss the importance of (1) reduction of uncertainty in local and hyper-local environments, (2) biocultural provocations in which birds fulfill important roles in human society, and (3) informational connectivity and locally-defined interspecies ethical relationships as key elements for inclusive and effective ecocultural bird conservation.
Vasoactive inotropic score as a predictor of mortality in neonatal septic shock
Authors: Demirhan Salih , Topcuoglu Sevilay , Karadag Nilgun , Ozalkaya Elif , Karatekin Guner 
Published: November 2022

Abstract

Background
Although many improvements in neonatal care have been achieved, mortality rates for sepsis and septic shock in newborns are still high. The vasoactive inotropic score (VIS) was designed and studied to predict mortality in different settings. There are currently no data on the predictive ability of the VIS for mortality in newborn patients with septic shock.

Methods
Patients with late-onset neonatal sepsis who required inotropes because of fluid-refractory septic shock during the study period were included in the study. Four distinct VIS values were calculated for each septic shock episode after inotropic treatment had begun, that is, at the initiation of inotropic treatment and at 24 and 48 h after inotropic treatment had begun, and the highest VIS (VISmax) at any time after initiation of inotropic agents.

Results
The 98 episodes studied were divided into two groups according to the outcomes of their sepsis episodes as survivors (n = 39) or nonsurvivors (n = 59). The areas under the curve of the VIS values for the prediction of mortality were the VISmax (0.819, p &lt; 0.001), followed by the VIS48 (0.802, p &lt; 0.001), VIS24 (0.762, p = 0.001) and VIS0 (0.699, p = 0.015). Patients with a VISmax of greater than 20 had significantly higher odds of mortality (p &lt; 0.001, β = 14.7, 95% confidence interval [4.7–45.9]).

Conclusion
We found that the VISmax was an easy-to-use and helpful tool for predicting a poor outcome in neonatal sepsis. Physicians should be aware that the prognosis is poor for any newborn with a VIS of 20 or greater at any point after the onset of sepsis.
USPSTF colorectal cancer screening update 2021
Authors: Klimkiewicz Pawel 
Published: November 2022

Abstract:
The US Preventive Services Task Force recently expanded its colorectal cancer screening recommendations to start screening adults with average risk profile at age 45. In the face of rising healthcare costs, limited medical resources, and in order to facilitate shared decision-making conversations, primary care clinicians should have a thorough understanding of the evidence supporting this new screening guideline.
Diagnosis and Management of Cuffitis: A Systematic Review
Authors: Hembree Amy E. , Scherl Ellen 
Published: November 2022

BACKGROUND:
In patients with ulcerative colitis or familial adenomatous polyposis who develop neoplasia or fail medical therapy and require colectomy, restorative proctocolectomy with IPAA is often indicated. Although often well tolerated, IPAA can be complicated by cuffitis or inflammation of the remaining rectal cuff. Although much has been published on this subject, there is no clear and comprehensive synthesis of the literature regarding cuffitis.

METHODS:
Our systematic literature review analyzes 34 articles to assess the frequency, cause, pathogenesis, diagnosis, classification, complications, and treatment of cuffitis.

RESULTS:
Cuffitis occurs in an estimated 10.2% to 30.1% of pouch patients. Purported risk factors include rectal cuff length >2 cm, pouch-rectal anastomosis, stapled anastomosis, J-pouch configuration, 2- or 3-stage IPAA, preoperative Clostridium difficile infection, toxic megacolon, fulminant colitis, preoperative biologic use, medically refractory disease, immunomodulator/steroids use within 3 months of surgery, extraintestinal manifestations of IBD, and BMI <18.5 kg/m2 at the time of colectomy. Adverse consequences associated with cuffitis include decreased quality-of-life scores, increased risk for pouchitis, pouch failure, pouch excision, and pouch neoplasia.

CONCLUSIONS:
Given the similarities between pouchitis and cuffitis, diagnosis and treatment of cuffitis should proceed according to the International Ileal Pouch Consortium guidelines. This review found that the majority of the current literature fails to distinguish between classic cuffitis (a form of reminant ulcerative proctitis) and nonclassic cuffitis (resulting from other causes). Further work is needed to distinguish the unique risk factors and endoscopic characteristics associated with each subtype, and further randomized clinical trials should be conducted to strengthen the evidence for treatment options.
Effect of mechanical power on mortality in invasively ventilated ICU patients without the acute respiratory distress syndrome
Authors: van Meenen David M.P. , Algera Anna Geke , Schuijt Michiel T.U. , Simonis Fabienne D. , van der Hoeven Sophia M. , Neto Ary Serpa , Abreu Marcelo Gama de , Pelosi Paolo , Paulus Frederique , Schultz Marcus J. 
Published: November 2022

BACKGROUND
The mechanical power of ventilation (MP) has an association with outcome in invasively ventilated patients with the acute respiratory distress syndrome (ARDS). Whether a similar association exists in invasively ventilated patients without ARDS is less certain.

OBJECTIVE
To investigate the association of mechanical power with mortality in ICU patients without ARDS.

DESIGN
This was an individual patient data analysis that uses the data of three multicentre randomised trials.

SETTING
This study was performed in academic and nonacademic ICUs in the Netherlands.

PATIENTS
One thousand nine hundred and sixty-two invasively ventilated patients without ARDS were included in this analysis. The median [IQR] age was 67 [57 to 75] years, 706 (36%) were women.

MAIN OUTCOME MEASURES
The primary outcome was the all-cause mortality at day 28. Secondary outcomes were the all-cause mortality at day 90, and length of stay in ICU and hospital.

RESULTS
At day 28, 644 patients (33%) had died. Hazard ratios for mortality at day 28 were higher with an increasing MP, even when stratified for its individual components (driving pressure (P < 0.001), tidal volume (P < 0.001), respiratory rate (P < 0.001) and maximum airway pressure (P = 0.001). Similar associations of mechanical power (MP) were found with mortality at day 90, lengths of stay in ICU and hospital. Hazard ratios for mortality at day 28 were not significantly different if patients were stratified for MP, with increasing levels of each individual component.

CONCLUSION
In ICU patients receiving invasive ventilation for reasons other than ARDS, MP had an independent association with mortality. This finding suggests that MP holds an added predictive value over its individual components, making MP an attractive measure to monitor and possibly target in these patients.
TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02159196, ClinicalTrials.gov Identifier: NCT02153294, ClinicalTrials.gov Identifier: NCT03167580.
Performance of Paralympic Powerlifting Records Holders
Authors: Lopes-Silva João Paulo , Franchini Emerson , Kons Rafael 
Published: November 2022

Objective
This study was conducted to investigate the performance difference for current World (Junior and Senior) and Paralympic (Senior) record holders according to origin of impairment (acquired or congenital), level of competition, and sex and to describe the performance progression of Paralympic Powerlifting records holders.

Design
This retrospective cohort study involving 60 current world (20 Junior and 20 Senior) and Paralympic (20 Senior) Para powerlifting record holders with 15 males congenital impairment and 14 acquired impairment, while 18 females were acquired impairment and 9 congenital impairments.

Results
The origin of impairment did not influence the absolute and relative load of male and female recordists. However, for males, acquired athletes were older and heavier when compared with congenital athletes, but without differences for females. The absolute load of Junior World recordists was lower in relation to Senior World and Paralympic recordists independently of the sex. Congenital athletes more often reached the world record in the Junior category, while the acquired athletes were the ones who obtained most of the records in senior categories.

Conclusions
Our results show that origin of impairment did not influence the absolute and relative load of current World (Junior and Senior) and Paralympic (Senior) recordists.
Vaporized Nicotine (E-Cigarette) and Tobacco Smoking Among People With HIV: Use Patterns and Associations With Depression and Panic Symptoms
Authors: Hahn Andrew W. , Ruderman Stephanie A. , Nance Robin M. , Whitney Bridget W. , Eltonsy Sherif , Haidar Lara , Delaney Joseph A. C. , Drumright Lydia N. , Ma Jimmy , Mayer Kenneth H. , 'Cleirigh Conall O. , Napravnik Sonia , Eron Joseph J. , Christopoulos Katerina , Bamford Laura , Cachay Edward , Jacobson Jeffrey M. , Willig Amanda , Cropsey Karen , Chander Geetanjali , Crane Heidi M. , Fredericksen Rob J. 
Published: November 2022

Background:
Vaporized nicotine (VN) use is increasing among people with HIV (PWH). We examined demographics, patterns of use, depression, and panic symptoms associated with VN and combustible cigarette (CC) use among PWH.

Methods:
We analyzed VN use among PWH in care at 7 US sites. PWH completed a set of patient-reported outcomes, including substance use and mental health. We categorized VN use as never vs. ever with the frequency of use (days/month) and CC use as never, former, or current. We used relative risk regression to associate VN and CC use, depression, and panic symptoms. Linear regression estimated each relationship with VN frequency. Models were adjusted for demographics.

Results:
Among 7431 PWH, 812 (11%) reported ever-using VN, and 264 (4%) reported daily use. Half (51%) of VN users concurrently used CC. VN users were more likely than those without use to be younger, to be White, and to report ever-using CC. PWH reporting former CC use reported ≥8.5 more days per month of VN use compared with never CC use [95% confidence interval (95% CI): 5.5 to 11.5 days/month] or current CC use (95% CI: 6.6 to 10.5 days/month). Depression (relative risk: 1.20 [95% CI: 1.02 to 1.42]) and panic disorder (1.71 [95% CI: 1.43 to 2.05]) were more common among PWH ever-using VN. Depression was common among PWH using VN (27%) and CC (22%), as was panic disorder (21% for VN and 16% for CC).

Conclusion:
Our study elucidated demographic associations with VN use among PWH, revealed the overlap of VN and CC use, and associations with depression/panic symptoms, suggesting roles of VN in self-medication and CC substitution, warranting further longitudinal/qualitative research.
Phylogeography of the pallid ground squirrel (Spermophilus pallidicaudaSatunin, 1903) as a consequence of Holocene changes in the Mongolian steppe ecosystems
Authors: Kapustina Svetlana , Adiya Yansanjav , Lyapunova Elena , Brandler Oleg 
Published: November 2022

ABSTRACTThe influence of Quaternary climatic changes is a source of intraspecific genetic heterogeneity of faunal components of Asian steppe and semi-desert ecosystems. The pallid ground squirrelSpermophilus pallidicaudais a typical representative of Inner Asian Marmotini, the intraspecific structure of which remained unstudied to date. We studied for the first time the genetic structure of the pallid ground squirrel based on cytochromeband control region of mitochondrial DNA variability. We generated ecological niche models to estimate the current and past habitat suitability forS. pallidicauda. Our results revealed two phyletic lineages dividing this species into western and eastern population groups. According to our proposed reconstruction of the history ofS. pallidicaudadistribution, the divergence of the detected phyla may have resulted from the formation of the ecological barrier that separated the western and eastern parts of the range in the early Holocene. The hypothesis of the origin and life history ofS. pallidicaudais given.
Results of a phase Ib study of SB-121, an investigational probiotic formulation, in participants with autism spectrum disorder
Authors: Schmitt Lauren M. , Smith Elizabeth G. , Pedapati Ernest V. , Horn Paul , Will Meredith , Lamy Martine , Barber Lillian , Trebley Joe , Meyer Kevin , Heiman Mark , West Korbin H.J. , Hughes Phoevos , Ahuja Sanjeev , Erickson Craig A. 
Published: November 2022

AbstractAutism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by core impairments in social communication as well as restricted, repetitive patterns of behavior and/or interests. Individuals with ASD, which includes about 2% of the US population, have challenges with activities of daily living and suffer from comorbid medical and mental health concerns. While aripiprazole and risperidone are indicated for use in autistic youth with interfering irritability, there are no drugs indicated for the core impairments of ASD. As such, there is a significant need for the development of new medication strategies for individuals with ASD. This first-in-human placebo-controlled, double-blind, crossover study investigated the safety (primary objective) and efficacy of oral SB-121, a combination ofL. reuteri, Sephadex®(dextran microparticles), and maltose administered once daily for 28 days in 15 autistic participants. SB-121 was safe and well tolerated. SB-121-associated directional improvements in adaptive behavior measured by Vineland-3 and social preference as measured with eye tracking were noted. These results provide support for further clinical evaluation of SB-121 as a treatment in autistic patients.