bluuebunny/crossref_metadata_2025_split huggingface dataset:
A short review on transition metal chalcogenides/carbon nanocomposites for energy storage
Authors: Salarizadeh Parisa , Rastgoo-Deylami Mohadese , Askari Mohammad Bagher , hooshyari Khadijeh 
Published: July 2022

Abstract
Introducing suitable electrode materials and electrolytes for supercapacitors and next-generation batteries should be considered for the industrial application of these devices. Among the proposed materials for them, transition metal chalcogenides (TMCs), are attractive and efficient options due to their unique properties such as appropriate layered structure, good oxidation state of transition metals, high thermal and mechanical stabilities, etc. However, applying other layered materials with high electrical conductivity e.g. carbon-based materials can lead to producing remarkable results for the mentioned applications. However, an interesting point is how making TMCs composite with different types of carbon materials leads to improve electrochemical and structural properties of TMCs as active materials. In the present short review, the structural and electrochemical improvements of different types of TMC composites with carbon-based materials and their mechanism are investigated for supercapacitors and next-generation rechargeable batteries.
Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data
Authors: Junttila Sini , Smolander Johannes , Elo Laura L 
Published: July 2022

Abstract
Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of thousands of cells simultaneously and study transcriptomic changes between cells. scRNA-seq datasets increasingly include multisubject, multicondition experiments to investigate cell-type-specific differential states (DS) between conditions. This can be performed by first identifying the cell types in all the subjects and then by performing a DS analysis between the conditions within each cell type. Naïve single-cell DS analysis methods that treat cells statistically independent are subject to false positives in the presence of variation between biological replicates, an issue known as the pseudoreplicate bias. While several methods have already been introduced to carry out the statistical testing in multisubject scRNA-seq analysis, comparisons that include all these methods are currently lacking. Here, we performed a comprehensive comparison of 18 methods for the identification of DS changes between conditions from multisubject scRNA-seq data. Our results suggest that the pseudobulk methods performed generally best. Both pseudobulks and mixed models that model the subjects as a random effect were superior compared with the naïve single-cell methods that do not model the subjects in any way. While the naïve models achieved higher sensitivity than the pseudobulk methods and the mixed models, they were subject to a high number of false positives. In addition, accounting for subjects through latent variable modeling did not improve the performance of the naïve methods.
An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections
Authors: Oba Utako , Kohashi Kenichi , Sangatsuda Yuhei , Oda Yoshinao , Sonoda Koh-Hei , Ohga Shouichi , Yoshimoto Koji , Arai Yasuhito , Yachida Shinichi , Shibata Tatsuhiro , Ito Takashi , Miura Fumihito 
Published: July 2022

AbstractWith the advent of new molecular diagnostic techniques, retrieving DNA from the formalin-fixed paraffin-embedded (FFPE) tissues has become an essential yet challenging step for efficient downstream processes. Owing to low quality and quantity of DNA retrieved from the FFPE sections, the process is often impractical and needs significant improvements. Here, we established an efficient method for the purification of DNA from FFPE specimens by optimizing incubation temperature, incubation time, and the concentration of a formalin scavenger tris(hydroxymethyl)aminomethane (Tris) for reverse-crosslinking. The optimized method, named “Highly concentrated Tris-mediated DNA extraction” (HiTE), yielded three times the DNA yield per tissue slice compared with a representative DNA extraction kit. Moreover, the use of HiTE-extracted DNA increased the yield of the sequencing library three times and accordingly yielded a log higher and more reproducible sequencing library compared with that obtained using the commonly used commercial kit. The sequencing library prepared from HiTE-extracted FFPE-DNA had longer inserts and produced reads that evenly covered the reference genome. Successful application of HiTE-extracted FFPE-DNA for whole-genome and targeted gene panel sequencing indicates its practical usability.
The New Validity Rules in Chinese Civil Code and Chinese State-owned Enterprises’ Freedom in Contracting: One Step Too Far
Authors: Jiang Hao , von Appen Antonia 
Published: July 2022

Abstract
Upon the enactment of Chinese Civil Code, the previous rules that allowed for enlarged state power to annul contracts such as General Principles of Civil Law article 58 §3 and Contract Law article 52 §1-§2 were dropped. Chinese law has gone one step further in promoting freedom of contract. The validity rules now have been streamlined and the previous contradictory and inconsistent treatment between civil juristic acts and contracts, state and private parties eliminated. However, the new legislative technique will unavoidably facilitate asset stripping, the very reason that the paternalistic rules were in place. Through a historical, doctrinal and logical lens, we will show why there can be no effective model of a neutral set of validity rules that could deal with state-owned enterprises in a less than free and competitive market. The only way to make it work is to have SOEs exit most of the competitive industries and focus on areas that serve the policy goals. Also, paternalistic rules concerning the validity of a contract in trading state-assets should be enacted either in the Civil Code or through special legislations and applicable to government, state-owned enterprises and private parties alike.
Early and late readmissions after enhanced recovery thoracoscopic lobectomy
Authors: Huang Lin , Frandsen Mikkel Nicklas , Kehlet Henrik , Petersen René Horsleben 
Published: July 2022

Abstract

OBJECTIVES
The purpose of this study was to describe the incidence of and reasons for early (0–30 days) and late (31–90 days) readmissions after enhanced recovery video-assisted thoracoscopic surgery lobectomy.

METHODS
We performed a retrospective analysis of prospectively collected consecutive VATS lobectomy data in an institutional database from January 2019 through December 2020. All reasons for readmission with complete follow-up were individually evaluated. Univariable and multivariable analyses were used to assess predictors.

RESULTS
In total, 508 patients were included; the median length of stay after the operation was 3 days. There were 77 (15%) early and 54 (11%) late readmissions, respectively. There were 33 (7%) multiple readmissions during postoperative days 0–90 ; pneumonia (19.8%) and pneumothorax (18.3%) were the dominant reasons for early readmissions, and the side effects of adjuvant chemotherapy (22.0%), for late readmissions. In multivariable analyses, current smoking (P = 0.001), alcohol abuse (P = 0.024) and chronic obstructive pulmonary disease (P = 0.019) were predictors of early readmissions, whereas Clavien-Dindo I-II grade gastrointestinal complications predicted late readmissions (P = 0.006) and multiple readmissions (P = 0.007). Early discharge (&lt; 3 days) was not a predictor of readmissions. Early readmission did not increase late readmission.

CONCLUSIONS
Early and late readmissions after video-assisted thoracoscopic lobectomy are frequent even when enhanced recovery programmes are followed. Pulmonary complications and adjuvant chemotherapy are the most predominant reasons for early and late readmissions.
Analysis of transcriptome data and quantitative trait loci enables the identification of candidate genes responsible for fiber strength in Gossypium barbadense
Authors: Duan Yajie , Chen Qin , Chen Quanjia , Zheng Kai , Cai Yongsheng , Long Yilei , Zhao Jieyin , Guo Yaping , Sun Fenglei , Qu Yanying 
Published: July 2022

Abstract
Gossypium barbadense possesses a superior fiber quality because of its fiber length and strength. An in-depth analysis of the underlying genetic mechanism could aid in filling the gap in research regarding fiber strength and could provide helpful information for Gossypium barbadense breeding. Three quantitative trait loci related to fiber strength were identified from a Gossypium barbadense recombinant inbred line (PimaS-7 × 5917) for further analysis. RNA sequencing was performed in the fiber tissues of PimaS-7 × 5917 0–35 days postanthesis. Four specific modules closely related to the secondary wall-thickening stage were obtained using the weighted gene coexpression network analysis. In total, 55 genes were identified as differentially expressed from 4 specific modules. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for enrichment analysis, and Gbar_D11G032910, Gbar_D08G020540, Gbar_D08G013370, Gbar_D11G033670, and Gbar_D11G029020 were found to regulate fiber strength by playing a role in the composition of structural constituents of cytoskeleton and microtubules during fiber development. Quantitative real-time PCR results confirmed the accuracy of the transcriptome data. This study provides a quick strategy for exploring candidate genes and provides new insights for improving fiber strength in cotton.
Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages
Authors: Cerón-Romero Mario A , Fonseca Miguel M , de Oliveira Martins Leonardo , Posada David , Katz Laura A 
Published: July 2022

Abstract
Advances in phylogenomics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single-gene fusion. Subsequent, highly cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes does not consider phylogenetically-informative events like gene duplications and losses. A recent study using gene tree parsimony (GTP) suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we use GTP with a duplication-loss model in a gene-rich and taxon-rich dataset (i.e., 2,786 gene families from two sets of 155 and 158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We also contrasted our results and discarded alternative hypotheses from the literature using GTP and the likelihood-based method SpeciesRax. Our estimates suggest a root between Fungi or Opisthokonta and all other eukaryotes; but based on further analysis of genome size, we propose that the root between Opisthokonta and all other eukaryotes is the most likely.
Chromosome-Scale Genome Assembly of the Hexaploid Taiwanese Goosefoot “Djulis” (Chenopodium formosanum)
Authors: Jarvis David E , Sproul John S , Navarro-Domínguez Beatriz , Krak Karol , Jaggi Kate , Huang Yung-Fen , Huang Tzu-Yun , Lin Tzu Che , Jellen Eric N , Maughan Peter J 
Published: July 2022

Abstract
Djulis (Chenopodium formosanum Koidz.) is a crop grown since antiquity in Taiwan. It is a BCD-genome hexaploid (2n = 6x = 54) domesticated form of lambsquarters (C. album L.) and a relative of the allotetraploid (AABB) C. quinoa. As with quinoa, djulis seed contains a complete protein profile and many nutritionally important vitamins and minerals. While still sold locally in Taiwanese markets, its traditional culinary uses are being lost as diets of younger generations change. Moreover, indigenous Taiwanese peoples who have long safeguarded djulis are losing their traditional farmlands. We used PacBio sequencing and Hi-C-based scaffolding to produce a chromosome-scale, reference-quality assembly of djulis. The final genome assembly spans 1.63 Gb in 798 scaffolds, with 97.8% of the sequence contained in 27 scaffolds representing the nine haploid chromosomes of each sub-genome of the species. Benchmarking of universal, single-copy orthologs indicated that 98.5% of the conserved orthologous genes for Viridiplantae are complete within the assembled genome, with 92.9% duplicated, as expected for a polyploid. A total of 67.8% of the assembly is repetitive, with the most common repeat being Gypsy long terminal repeat retrotransposons, which had significantly expanded in the B sub-genome. Gene annotation using Iso-Seq data from multiple tissues identified 75,056 putative gene models. Comparisons to quinoa showed strong patterns of synteny which allowed for the identification of homoeologous chromosomes, and sub-genome-specific sequences were used to assign homoeologs to each sub-genome. These results represent the first hexaploid genome assembly and the first assemblies of the C and D genomes of the Chenopodioideae subfamily.
Increasing Pain Interference Is Associated With Cognitive Decline Over Four Years Among Older Puerto Rican Adults
Authors: Milani Sadaf Arefi , Bell Tyler R , Crowe Michael , Pope Caitlin N , Downer Brian 
Published: July 2022

Abstract

Background
Pain is associated with cognitive decline among older adults, but few studies have investigated bidirectional associations between pain and cognitive decline, especially in older Hispanic populations. Our objective was to assess the bidirectional association between pain interference and cognitive performance in a sample of older Puerto Rican adults.

Methods
Data came from baseline and 4-year follow-up of the Puerto Rican Elderly: Health Conditions Study, a longitudinal representative study of Puerto Rican older adults aged 60 and older. Pain and cognitive performance were assessed at each wave. A pain interference variable was created using the sum of pain status (yes/no) and pain interference (yes/no; range 0–2). Global cognitive performance was assessed with the Mini-Mental Cabán. We tested bidirectional associations using a path model with concurrent and cross-lagged paths between pain and cognitive performance, adjusting for sociodemographic and health factors (n = 2 349).

Results
Baseline pain interference was not associated with baseline cognitive performance (p = .636) or with cognitive performance at follow-up (p = .594). However, increased pain interference at follow-up was associated with greater cognitive decline at follow-up (β = −0.07, standard error [SE] = 0.02, p = .003). Greater baseline cognitive performance was associated with lower pain interference at follow-up (β = −0.07, SE = 0.02, p = .007).

Conclusions
These findings highlight the importance of worsening pain interference as a potentially modifiable risk factor for cognitive decline, as pain treatment options exist. Additionally, better baseline cognitive performance may be a protective factor for pain, providing further evidence of the dynamic relationship between pain and cognitive performance.
Patient-Reported Barriers and Enablers to Deprescribing Recommendations During a Clinical Trial (Shed-MEDS)
Authors: Kim Jennifer L , Lewallen Kanah M , Hollingsworth Emily K , Shah Avantika S , Simmons Sandra F , Vasilevskis Eduard E 
Published: July 2022

AbstractBackground and ObjectivesEffective deprescribing requires shared decision making between a patient and their clinician, and should be used when implementing evidence-based deprescribing conversations. As part of the Shed-MEDS clinical trial, this study assessed barriers and enablers that influence patient decision making in deprescribing to inform future implementation efforts and adaptations.Research Design and MethodsShed-MEDS, a randomized controlled deprescribing trial, included hospitalized older adults discharging to post-acute care facilities. A trained clinician reviewed each participant’s medical history and medication list to identify medications with potential for deprescribing. The study clinician then conducted a semistructured patient-centered deprescribing interview to determine patient (or surrogate) concerns about medications and willingness to deprescribe. Reeve et al.’s (2013) framework was used to categorize barriers and enablers to deprescribing from the patient’s perspective, including “appropriateness of cessation,” “fear,” “dislike of a medication,” “influences,” and “process of cessation.”ResultsOverall, participants/surrogates (N = 177) agreed with 63% (883 total medications) of the study clinician’s deprescribing recommendations. Thematic analysis revealed that “appropriateness” of a medication was the most common barrier (88.2%) and enabler (67.3%) to deprescribing. Other deprescribing enablers were in the following domains: “influences” (22.7%), “process” (22.5%), “pragmatic” (19.4%), and “dislike” (5.3%).Discussion and ImplicationsUse of a semistructured deprescribing interview conversation tool allowed study clinicians to elicit individual barriers and enablers to deprescribing from the patient’s perspective. Participants in this study expressed more agreement than disagreement with study clinicians’ deprescribing recommendations. These results should inform future implementation efforts that incorporate a patient-centered framework during deprescribing conversations.Clinical Trials Registration NumberNCT02979353
Saving Ukrainian Lives During the Russian War: Ukraine Must Waive IP Rights under Article 73 TRIPS to Provide Access to Essential Medicines
Authors: Gurgula Olga 
Published: July 2022

Abstract
In light of the severity of the health crisis in Ukraine due to the Russian aggression, the Ukrainian government must urgently implement expeditious solutions to increase the supply of essential medicines and medical products. One such measure is to exploit all existing domestic manufacturing capacities that are still intact and seek any potential possibility to import essential medicines from abroad. For this, all the barriers would need to be eliminated, including those in the form of intellectual property (IP) rights that might protect many essential medicines that are currently needed in Ukraine. This article argues that the existing mechanism of compulsory licensing under TRIPS and Ukrainian IP law is not effective to resolve the problem of access to medicines during such a critical situation as the ongoing war. It therefore suggests that Ukraine must immediately waive all IP rights related to essential medicines and medical products to enable the domestic production and seek any potential import of generics and biosimilars of essential medicines. Such a waiver would be justified based on ‘security exceptions’ of Art. 73(b)(iii) TRIPS. This provision allows a WTO member to utilise measures to protect its essential security interests taken in time of war. It is hoped that this article will provide guidance to the Ukrainian government on the most effective way to deal with the current health crisis in Ukraine and, thus, would help to save lives of millions of people in Ukraine that suffer from Russia’s unjustified, horrific aggression.
Increased Expression of Interleukin-13 Receptor in Ileum Associated With Nonresponse to Adalimumab in Ileal Crohn’s Disease
Authors: Wong Emily C L , Yusuf Arif , Pokryszka Jagoda , Dulai Parambir S , Colombel Jean-Frederic , Marshall John K , Reinisch Walter , Narula Neeraj 
Published: July 2022

Abstract

Background
The terminal ileum poses a predilection for Crohn’s disease (CD) but is less susceptible to undergo healing to treatment with biologics and small molecules. This study aimed to evaluate histologic features associated with endoscopic remission (ER).

Methods
This is a post hoc analysis of patients with moderately to severely active CD, defined as Crohn’s disease activity index 220 to 450, and terminal ileal ulceration treated with antitumor necrosis factor (TNF)-α inhibitor adalimumab from the EXTEND trial. We studied whether baseline total Global Histologic Disease Activity Scores (GHAS), any individual histologic element, and specific immunohistochemical (IHC) markers of chronic inflammation from biopsy specimens were associated with postinduction (week 12) and maintenance (week 52) ER, defined as Simple Endoscopic Score for Crohn’s Disease of 0. Multivariable logistic regression models adjusted for confounders were used to assess the relationship between histologic markers and 1-year outcomes.

Results
Seventy-one adult patients with CD affecting the ileum were included in this analysis. Both baseline ileal GHAS scores and individual histologic components were not found to be associated with ER at weeks 12 or 52. Increased expression of interleukin-13 receptor (IL-13R) on IHC stains was associated with reduced likelihood of achieving 1-year ER (adjusted odds ratio, 0.06; 95% CI, 0.01-0.92; P = .044). No other biomarker assessed was associated with 1-year ER.

Conclusions
Ileal histologic disease activity and IHC activation markers of chronic mucosal inflammation were not associated with 1-year ER. However, strong staining for IL-13 receptor in the ileum was associated with reduced odds of 1-year ER using adalimumab. Mucosal cellular disease profiles might pose an opportunity to guide treatment of CD.
5-HT5A Receptor Antagonist ASP5736 Ameliorates Several Abnormal Behaviors in an Fmr1-Targeted Transgenic Male Rat Model of Fragile X Syndrome
Authors: Yamazaki Mayako , Arai Takatomo , Yarimizu Junko , Matsumoto Mitsuyuki 
Published: July 2022

Abstract

Background
Fragile X syndrome (FXS) is a genetic condition that causes a range of developmental problems, including intellectual disability, aggressive behavior, anxiety, abnormal sensory processing, and cognitive impairment. Despite intensive preclinical research in Fmr1-targeted transgenic mice, an effective treatment for FXS has yet to be developed. We previously demonstrated that ASP5736, a 5-Hydroxytryptamine (serotonin) receptor 5A receptor antagonist, ameliorated scopolamine-induced working memory deficits in mice, reference memory impairment in aged rats, and methamphetamine-induced positive symptoms and phencyclidine-induced cognitive impairment in animal models of schizophrenia. We hypothesized that ASP5736 may be effective for ameliorating similar behavior deficits in male Fmr1-targeted transgenic rats as a preclinical model of FXS.

Methods
We evaluated the effect of acute oral administration of ASP5736 on the abnormal behavior of hyperactivity (0.01, 0.1 mg/kg), prepulse inhibition (0.01, 0.03, 0.1 mg/kg), and the novel object recognition task (0.1 mg/kg) in Frmr1-knockout (KO) rats.

Results
Fmr1-KO rats showed body weight gain, hyperactivity, abnormal sensory motor gating, and cognitive impairment. ASP5736 (0.1 mg/kg) reversed the hyperactivity and ameliorated the sensory motor gating deficits (0.03–0.1 mg/kg). ASP5736 (0.01 mg/kg) also improved cognitive impairment.

Conclusions
ASP5736 is a potential drug candidate for FXS. Further studies are needed to confirm its clinical efficacy.