bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genome-wide association study of survival in patients with sepsis
Authors: Hernandez-Beeftink Tamara , Guillen-Guio Beatriz , Lorenzo-Salazar Jose M. , Corrales Almudena , Suarez-Pajes Eva , Feng Rui , Rubio-Rodríguez Luis A. , Paynton Megan L. , Cruz Raquel , García-Laorden M. Isabel , Prieto-González Miryam , Rodríguez-Pérez Aurelio , Carriedo Demetrio , Blanco Jesús , Ambrós Alfonso , González-Higueras Elena , Espinosa Elena , Muriel Arturo , Tamayo Eduardo , Martin María M. , Lorente Leonardo , Domínguez David , de Lorenzo Abelardo García , Giannini Heather M. , Reilly John P. , Jones Tiffanie K. , Añón José M. , Soro Marina , Carracedo Ángel , Wain Louise V. , Meyer Nuala J. , Villar Jesús , Flores Carlos ,   the Genetics of Sepsis (GEN-SEP) Network
Published: November 2022

Abstract
Background
Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction and has a high mortality rate in adult intensive care units. Most genetic studies have identified gene variants associated with development and outcomes of sepsis focusing on biological candidates. We conducted the first genome-wide association study (GWAS) of 28-day survival in adult patients with sepsis.

Methods
This study was conducted in two stages. The first stage was performed on 687 European sepsis patients from the GEN-SEP network and 7.5 million imputed variants. Association testing was conducted with Cox regression models, adjusting by sex, age, and the main principal components of genetic variation. A second stage focusing on the prioritized genetic variants was performed on 2,063 ICU sepsis patients (1362 European Americans and 701 African-Americans) from the MESSI study. A meta-analysis of results from the two stages was conducted and significance was established at p < 5.0 × 10−8. Whole-blood transcriptomic, functional annotations, and sensitivity analyses were evaluated on the identified genes and variants.

Findings
We identified three independent low-frequency variants associated with reduced 28-day sepsis survival, including a missense variant in SAMD9 (hazard ratio [95% confidence interval] = 1.64 [1.37–6.78], p = 4.92 × 10−8). SAMD9 encodes a possible mediator of the inflammatory response to tissue injury.

Interpretation
We performed the first GWAS of 28-day sepsis survival and identified novel variants associated with reduced survival. Larger sample size studies are needed to better assess the genetic effects in sepsis survival and to validate the findings.
COVID-19-Related manuscripts: lag from preprint to publication
Authors: Drzymalla Emily , Yu Wei , Khoury Muin J. , Gwinn Marta 
Published: November 2022

Abstract
Objective
Preprints have had a prominent role in the swift scientific response to COVID-19. Two years into the pandemic, we investigated how much preprints had contributed to timely data sharing by analyzing the lag time from preprint posting to journal publication.

Results
To estimate the median number of days between the date a manuscript was posted as a preprint and the date of its publication in a scientific journal, we analyzed preprints posted from January 1, 2020, to December 31, 2021 in the NIH iSearch COVID-19 Portfolio database and performed a Kaplan-Meier (KM) survival analysis using a non-mixture parametric cure model. Of the 39,243 preprints in our analysis, 7712 (20%) were published in a journal, after a median lag of 178 days (95% CI: 175–181). Most of the published preprints were posted on the bioRxiv (29%) or medRxiv (65%) servers, which allow authors to choose a subject category when posting. Of the 20,698 preprints posted on these two servers, 7358 (36%) were published, including approximately half of those categorized as biochemistry, biophysics, and genomics, which became published articles within the study interval, compared with 29% categorized as epidemiology and 26% as bioinformatics.
Hospital-prepared low-dose atropine eye drops for myopia progression control using atropine sulfate injection diluted in normal saline and lubricants
Authors: Wongwirawat Nuthida , Kuchonthara Nirachorn , Boontanomwong Sorrawit , Pongpirul Krit 
Published: November 2022

Abstract
Objective
As low-dose atropine eye-drops for myopia progression control prepared in-house by diluting the commercial 0.1% atropine eye-drop with sterile water or normal saline has been a common practice whereas atropine injection is readily available and could be a more feasible alternative, this study aimed to assess the properties of the in-house low-dose atropine eye-drops prepared by diluting the atropine injection in two solvents and tested in two temperature conditions.

Results
The 0.01% atropine eye-drops contains no bacteria, fungi, or particulate matter. The levels of atropine sulfate on all samples were comparable to the freshly prepared samples at the 12th week, regardless of the solvents used or storage conditions. The low-dose atropine eye-drops prepared from readily available atropine sulfate injection at healthcare facilities could be an alternative to commercial products.
Diagnosis of tuberculosis with autoimmune hepatitis–systemic lupus erythematosus overlap syndrome: a case report
Authors: Shekhar  , Gupta Nikita Yogesh , Harisingani Avi Ravi 
Published: November 2022

Abstract
Background
There is ample evidence indicating that immunosuppressive therapy or immune dysregulation in systemic lupus erythematosus increases the risk for tuberculosis. Interestingly, a few case reports suggest that tuberculosis could also be a risk factor for systemic lupus erythematosus and other autoimmune diseases.

Case presentation
We report the case of a 32-year-old Indian patient who was co-diagnosed with tuberculosis, systemic lupus erythematosus, and autoimmune hepatitis without any history of prior immunosuppression. This stresses the complex relationship between tuberculosis and autoimmune diseases.

Conclusion
Further research is warranted in this field to unfold the complex relationship between tuberculosis and systemic lupus erythematosus. It is essential to establish clear guidelines for the management of coexisting tuberculosis and systemic lupus erythematosus to promote individualized treatment.
Electroacupuncture as an effective therapy for Tapia’s syndrome after transoral intubation for general anesthesia: a case report and review of the literature
Authors: Xie Luan , Xiong Zhenyu , Xiao Weihong , Mo Yingnan , Li Xiangliang , Zhuang Xuan , Yang Ying , Jin Haipeng 
Published: November 2022

Abstract
Background
Tapia’s syndrome is a rare complication of airway manipulation under general anesthesia. Injuries to the vagus nerve (X) and hypoglossal nerve (XII) during transoral intubation are the primary cause of the disease. The typical symptoms include hoarseness, dysarthria, dysphagia, tongue muscle atrophy, and tongue deviation toward the affected side. We report a case of Tapia’s syndrome treated with electroacupuncture to accelerate the recovery process, and discuss the potential mechanism behind our findings based on previous research.

Case presentation
In this report, we describe a 57-year-old Chinese man who suffered Tapia’s syndrome after craniotomy evacuation of hematoma with general anesthesia and transoral intubation. After 52 days of electroacupuncture therapy along with standard swallowing training, the patient achieved significant improvement in deglutition and speech function.

Conclusion
Electroacupuncture is effective and safe for Tapia’s syndrome. It can shorten the recovery time when combined with routine swallowing rehabilitation.
ALDH2 gene polymorphism is associated with fitness in the elderly Japanese population
Authors: De Almeida Kathleen Yasmin , Saito Mika , Homma Hiroki , Mochizuki Yukina , Saito Aoto , Deguchi Minoru , Kozuma Ayumu , Okamoto Takanobu , Nakazato Koichi , Kikuchi Naoki 
Published: November 2022

Abstract
Purpose
The aldehyde dehydrogenase 2 (ALDH2) rs671 polymorphism, which is exclusive to the Asian population, is related to many diseases. A high reactive oxygen species production in mitochondria, and low muscle strength in athletes and non-athletes, has been observed, as our previous study demonstrated. The purpose of this research was to investigate the influence of ALDH2 rs671 on the loss of muscle strength with aging and replicate our previous study in non-athletes.

Methods
Healthy Japanese individuals (n = 1804) aged 23–94 years were genotyped using DNA extracted from saliva. Muscle strength was assessed using grip strength and chair stand test (CST). The interaction between age and genotypes was analyzed by two-way analysis of covariance (ANCOVA) adjusted for sex, body mass index (BMI), and exercise habit.

Results
Individuals aged ≧55 with the AA genotype had a lower performance than those with the GG + GA genotype in the grip strength test (28.1 ± 9.1 kg vs. 29.1 ± 8.3 kg, p = 0.021). There was an interaction between age and genotype, where individuals with ≧55 years old AA genotype had a higher loss of strength compared to GG + GA genotypes in the CST (0.025). No interaction in other models and no sex differences were found.

Conclusion
This study replicated previous results of the relationship between the AA genotype with lower muscle strength and as a novelty showed that this genotype is associated with a higher age-related loss of strength.
A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata
Authors: Aubé Johanne , Cambon-Bonavita Marie-Anne , Velo-Suárez Lourdes , Cueff-Gauchard Valérie , Lesongeur Françoise , Guéganton Marion , Durand Lucile , Reveillaud Julie 
Published: November 2022

AbstractBackgroundIn deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimpRimicaris exoculatais fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential.ResultsWe reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages ofHepatoplasmataceaeandDeferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules,Deferribacteresshowed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition,Deferribactereswere observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this.ConclusionOverall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of theRimicarisholobiont.
Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts
Authors: Luo Xiao-Qing , Wang Pandeng , Li Jia-Ling , Ahmad Manzoor , Duan Li , Yin Ling-Zi , Deng Qi-Qi , Fang Bao-Zhu , Li Shan-Hui , Li Wen-Jun 
Published: November 2022

AbstractBackgroundViral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts’ metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments.ResultsHere, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders.ConclusionsOverall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions.
Two cases of left ventricular apical aneurysm associated with severe aortic stenosis: case report
Authors: Koga Yuichi , Kamohara Keiji , Nogami Eijiro , Shimauchi Kouta , Takeuchi Yuki , Uchino Motonori , Morokuma Hiroyuki , Koga Shugo , Yunoki Junji 
Published: November 2022

Abstract
Background
Left ventricular (LV) apical aneurysm associated with aortic valve stenosis (AS) is very rare. We herein report two cases of this entity.

Case presentation
Case 1 was a 75-year-old woman admitted for surgery for severe AS and enlargement of the ascending aorta. Preoperative routine echocardiography and cardiac computed tomography (CT) revealed an unexpected local aneurysm of the LV apex. The patient underwent aortic valve replacement (AVR), LV aneurysm resection, and ascending aorta replacement. Case 2 was a 71-year-old woman diagnosed with severe AS. Preoperative cardiac CT detected LV apical aneurysm that could not be detected by echocardiography. Cardiac catheterization showed a coronary ventricular fistula. The patient underwent AVR and LV aneurysm resection. Given that neither of the two cases had a history of myocardial infarction or obstructive hypertrophic cardiomyopathy, the cause of the local aneurysm of the LV apex was thought to be relative ischemia at the apex due to myocardial hypertrophy and LV pressure overload due to long-term AS. In addition, a coronary artery fistula was suggested to be involved in the relative ischemia of the apex in Case 2.

Conclusions
Echocardiography alone is not sufficient to exclude apical aneurysm, and cardiac CT may be useful. Regarding the surgical indication, it is necessary to consider further cases in the future.
The First Compound Heterozygous Mutations ofDMP1Causing Rare Autosomal Recessive Hypophosphatemic Rickets Type 1
Authors: Ni Xiaolin , Gong Yiyi , Jiang Yan , Li Xiang , Pang Qianqian , Liu Wei , Chi Yue , Jiajue Ruizhi , Wang Ou , Li Mei , Xing Xiaoping , Xia Weibo 
Published: November 2022

AbstractContextHereditary hypophosphatemic rickets (HR) consists of a group of inherited hypophosphatemia due to mutations of different genes, which need genetic analysis to make a differential diagnosis. Among them, autosomal recessive hypophosphatemic rickets type 1 (ARHR1), caused by a homozygous mutation of dentin matrix protein 1 (DMP1), is extremely rare, with only 30 reported patients. To date, there has been no case with compound heterozygous DMP1 mutations.ObjectiveTo report the first compound heterozygous mutations of DMP1 causing ARHR1 and confirm the effect of the mutation on DMP1 protein.MethodsWe report the clinical features of a Chinese patient with HR. Whole-exome sequencing (WES) was performed on the proband. Then, Cytoscan HD array, Sanger sequencing, and genomic quantitative PCR (qPCR) were used to confirm the mutations. A cell experiment was conducted to explore the effect of the mutation.ResultsThe proband is a 4-year-old boy, who developed genu varum when he was able to walk at age 1 year and tooth loss after a mild hit at age 3.5 years. Physical examination, biochemical measurement, and imaging finding indicated HR. Family history was negative. WES performed on the proband revealed a novel start codon mutation (c.1A &gt; T, p.Met1Leu) in DMP1 and a large deletion involving most of the small integrin-binding ligand N-linked glycoprotein (SIBLING) family gene, including DSPP, DMP1, IBSP, and MEPE. The novel paternally inherited start codon mutation, which resulted in decreased expression of DMP1 protein with smaller molecular weight and cleavage defect, was confirmed by Sanger sequencing. The maternally inherited deletion was validated by Cytoscan and qPCR, and the breakpoint was finally identified by long-range PCR and Sanger sequencing. Manifestation of dentin dysplasia (DD) or dentinogenesis imperfecta (DGI) caused by DSPP mutations was absent in the patient and his mother, confirming that haploinsufficiency could not lead to DD or DGI.ConclusionWe report for the first time compound heterozygous DMP1 mutations consisting of a large deletion and a novel start codon mutation (c.1A &gt; T, p.Met1Leu) in a Chinese patient with ARHR1.
Robust model-based control of a packed absorption column for the natural gas sweetening process
Authors: Romero-Bustamante Jorge A. , Zurita-Herrera Brenda M. , Gutiérrez-Limón Miguel Ángel , Hernandez-Martinez Eliseo 
Published: November 2022

Abstract
The sweetening units are the most important in natural gas processing. Packed bed absorption columns are widely used in the sweetening process; however, their operation and control are not simple due to their highly non-linear behavior derived from their distributed nature and interaction between multiple physical phenomena. In this work, two robust model-based control schemes are implemented to regulate the CO2 concentration at the outlet of a packed bed absorption column in the gas sweetening process. The model of an industrial-scale absorption column and the structure of the controllers, i) control based on modeling error compensation (MEC) ideas, and ii) nonlinear model predictive control (NMPC) are described. Numerical results show that the proposed robust model-based controllers can regulate the controlled variable to the desired reference despite external disturbances, set-point changes, and uncertainties in the absorption column model.
Sliding mode controller design based on simple closed loop set point experiment for higher order processes with dead time
Authors: Siddiqui Mohammad Atif , Nishat Anwar Md. , Haque Laskar Shahedul 
Published: November 2022

Abstract
In this work, a sliding mode controller (SLMC) design approach has been proposed based on second order plus dead time process (SOPDTP). The SOPDTP model of the industrial processes have been obtained by performing a simple closed-loop set-point experiment (CLSPE) having a proportional controller only. The operating procedure of SLMC comprises of continuous and discontinuous control law. The parameters of continuous control law are derived by considering SOPDTP parameters and using the root locus technique. The discontinuous control law parameters are obtained by minimizing a performance index with the help of grasshopper optimization technique. The proposed SLMC design method has been validated by considering several examples with higher order process having diverse dynamics. The performance improvement by the proposed method over the recently reported work has been observed under nominal, perturbed and noisy conditions.
Spanishlo que pasa es queand its variants in Getxo and Barcelona
Authors: Paasch-Kaiser Christine , Sinner Carsten 
Published: November 2022

AbstractThe Spanish constructionlo que pasa es que‘what happens is that’, ‘the thing is’ is used in a wide variety of contexts and with a range of different meanings. Linguistic research that has been carried out on this relatively common construction often fails to include empirically collected data and, as a result, the diasystematic markers thereof have only been described to a very limited extent. The main focus of this article is to investigate the use of the constructionlo que pasa es queand its phonetically reduced formslo que pasa queandlo quein two Spanish-language oral speech corpora collected in Getxo (Basque Country) and Barcelona (Catalonia). These data are used to carry out a quantitative and qualitative study of the presence or absence of this construction in both regions of language contact, something which has yet to be considered or systematically analysed in the relevant research. The study identifies a statistically relevant diatopic markedness of the formslo que pasa es que,lo que pasaandpasa quewhile also providing empirical proof for the pragmatic use of these constructions within the varieties investigated. Furthermore, it confirms the use of additional reduced forms of said constructions and describes their development.
«A praia está perto»: Zum Gebrauch des Verbsestarin Ausdrücken der statischen Lage im Portugiesischen
Authors: Bartens Angela , Kempas Ilpo 
Published: November 2022

AbstractThe article examines the use ofestarin Portuguese expressions of permanent location, which runs counter to normative grammar, according to whichserandficarshould appear in those cases. This use ofestaris not mentioned in grammatical descriptions, either. Yet, it occurs in contemporary Portuguese (both Portugal and Brazil). The same goes for the Portuguese- and Spanish-lexified creoles, some of which usetá/stá(< estar),to express location. However, almost all rely on a single verb in these contexts. The research question was studied empirically in a corpus (N=1,037) based on Google searches with seven exact phrases includingestar,ser, andficar, subsequently complemented with an analysis of two other Portuguese corpora. The results show thatestarappears in expressions of permanent location, both in Portugal (22,5%) and Brazil (17,5%). However, there is a statistically significant difference,ficarbeing more frequent in Brazil andserin Portugal. Moreover, the higher frequency ofestarin Portugal may indirectly explain the popularity officarin Brazil. In addition,estarappears in written nonfiction, pointing to expressions of the typeestar localizado/situadoas its possible origin, also taking into account that no instances of its use were found in older documents.