bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling zero inflation is not necessary for spatial transcriptomics
Authors: Zhao Peiyao , Zhu Jiaqiang , Ma Ying , Zhou Xiang 
Published: May 2022

Abstract
Background
Spatial transcriptomics are a set of new technologies that profile gene expression on tissues with spatial localization information. With technological advances, recent spatial transcriptomics data are often in the form of sparse counts with an excessive amount of zero values.

Results
We perform a comprehensive analysis on 20 spatial transcriptomics datasets collected from 11 distinct technologies to characterize the distributional properties of the expression count data and understand the statistical nature of the zero values. Across datasets, we show that a substantial fraction of genes displays overdispersion and/or zero inflation that cannot be accounted for by a Poisson model, with genes displaying overdispersion substantially overlapped with genes displaying zero inflation. In addition, we find that either the Poisson or the negative binomial model is sufficient for modeling the majority of genes across most spatial transcriptomics technologies. We further show major sources of overdispersion and zero inflation in spatial transcriptomics including gene expression heterogeneity across tissue locations and spatial distribution of cell types. In particular, when we focus on a relatively homogeneous set of tissue locations or control for cell type compositions, the number of detected overdispersed and/or zero-inflated genes is substantially reduced, and a simple Poisson model is often sufficient to fit the gene expression data there.

Conclusions
Our study provides the first comprehensive evidence that excessive zeros in spatial transcriptomics are not due to zero inflation, supporting the use of count models without a zero inflation component for modeling spatial transcriptomics.
Reducing the risk of Plasmodium vivax after falciparum infections in co-endemic areas—a randomized controlled trial (PRIMA)
Authors: Thriemer Kamala , Degaga Tamiru Shibru , Christian Michael , Alam Mohammad Shafiul , Ley Benedikt , Hossain Mohammad Sharif , Kibria Mohammad Golam , Tego Tedla Teferi , Abate Dagimawie Tadesse , Weston Sophie , Karahalios Amalia , Rajasekhar Megha , Simpson Julie A. , Rumaseb Angela , Mnjala Hellen , Lee Grant , Anose Rodas Temesgen , Kidane Fitsum Getahun , Woyessa Adugna , Baird Kevin , Sutanto Inge , Hailu Asrat , Price Ric N. 
Published: May 2022

Abstract
Background
Plasmodium vivax forms dormant liver stages that can reactivate weeks or months following an acute infection. Recurrent infections are often associated with a febrile illness and can cause a cumulative risk of severe anaemia, direct and indirect mortality, and onward transmission of the parasite. There is an increased risk of P. vivax parasitaemia following falciparum malaria suggesting a rationale for universal use of radically curative treatment in patients with P. falciparum malaria even in the absence of detectable P. vivax parasitaemia in areas that are co-endemic for both species.

Methods
This is a multicentre, health care facility-based, randomized, controlled, open-label trial in Bangladesh, Indonesia and Ethiopia. Patients with uncomplicated falciparum malaria, G6PD activity of ≥70% of the adjusted male median (AMM) and haemoglobin levels ≥8g/dl are recruited into the study and randomized to either receive standard schizonticidal treatment plus 7-day high dose primaquine (total dose 7mg/kg) or standard care in a 1:1 ratio. Patients are followed up weekly until day 63. The primary endpoint is the incidence risk of any P. vivax parasitemia on day 63. Secondary endpoints include incidence risk on day 63 of symptomatic P. vivax malaria and the risk of any P. falciparum parasitaemia. Secondary safety outcomes include the proportion of adverse events and serious adverse events, the incidence risk of severe anaemia (Hb<5g/dl and <7g/dl) and/or the risk for blood transfusion, the incidence risk of ≥ 25% fall in haemoglobin with and without haemoglobinuria, and the incidence risk of ≥ 25% fall in haemoglobin to under 7g/dl with and without haemoglobinuria.

Discussion
This study evaluates the potential benefit of a universal radical cure for both P. vivax and P. falciparum in different endemic locations. If found safe and effective universal radical cure could represent a cost-effective approach to clear otherwise unrecognised P. vivax infections and hence accelerate P. vivax elimination.

Trial registration
NCT03916003. Registered on 12 April 2019.
Structural and functional specificity of H3K36 methylation
Authors: Lam Ulysses Tsz Fung , Tan Bryan Kok Yan , Poh John Jia Xin , Chen Ee Sin 
Published: May 2022

AbstractThe methylation of histone H3 at lysine 36 (H3K36me) is essential for maintaining genomic stability. Indeed, this methylation mark is essential for proper transcription, recombination, and DNA damage response. Loss- and gain-of-function mutations in H3K36 methyltransferases are closely linked to human developmental disorders and various cancers. Structural analyses suggest that nucleosomal components such as the linker DNA and a hydrophobic patch constituted by histone H2A and H3 are likely determinants of H3K36 methylation in addition to the histone H3 tail, which encompasses H3K36 and the catalytic SET domain. Interaction of H3K36 methyltransferases with the nucleosome collaborates with regulation of their auto-inhibitory changes fine-tunes the precision of H3K36me in mediating dimethylation by NSD2 and NSD3 as well as trimethylation by Set2/SETD2. The identification of specific structural features and various cis-acting factors that bind to different forms of H3K36me, particularly the di-(H3K36me2) and tri-(H3K36me3) methylated forms of H3K36, have highlighted the intricacy of H3K36me functional significance. Here, we consolidate these findings and offer structural insight to the regulation of H3K36me2 to H3K36me3 conversion. We also discuss the mechanisms that underlie the cooperation between H3K36me and other chromatin modifications (in particular, H3K27me3, H3 acetylation, DNA methylation and N6-methyladenosine in RNAs) in the physiological regulation of the epigenomic functions of chromatin.
RETRACTED ARTICLE: Association of cord blood asprosin concentration with atherogenic lipid profile and anthropometric indices
Authors: Hussein Hanan Khudhair , Aubead Nassrin Malik , Kzar Hamzah H. , Karim Yasir Salam , Amin Ali H. , Al-Gazally Moaed E. , Ahmed Tousief Irshad , Jawad Mohammed Abed , Hammid Ali Thaeer , Jalil Abduladheem Turki , Mustafa Yasser Fakri , Saleh Marwan Mahmood , Heydari Hafez 
Published: May 2022

Abstract
Background
Elevated lipids in umbilical cord blood affect fetal programming, leading to a higher risk of developing cardiovascular disease in later life. However, the causes of changes in the lipid profile of umbilical cord blood are not clear yet. This study aimed for the first time to determine the association of asprosin concentration with TAG, TC, HDL-C, LDL-C concentrations and TAG/HDL-C, TC/HDL-C, LDL-C/HDL-C and non-HDL-C/HDL-C ratio in umbilical cord blood as well as newborn anthropometric indices. This cross-sectional study was based on 450 mother- newborn pairs of a birth cohort study in Sabzevar, Iran. Multiple linear regression was used to estimate the association of lipid concentration and lipid ratios as well as birth weight (BW), birth length (BL), head circumference (HC) and chest circumference (CC) with asprosin in cord blood samples controlled for the relevant covariates.

Result
In fully adjusted models, each 1 ng/mL increase in asprosin was associated with 0.19 (95% CI 0.06, 0.31, P < 0.01), 0.19 (95% CI 0.10, 0.29, P < 0.01), 0.17 (95% CI 0.09, 0.25, P < 0.01), 0.17 (95% CI 0.09, 0.25, P < 0.01), 0.01 (95% CI 0.00, 0.013, P < 0.01), 0.01 (95% CI 0.01, 0.01, P < 0.01), 0.01 (95% CI 0.01, 0.01, P < 0.01) and 0.01 (95% CI 0.01, 0.01, P < 0.01) increase in TAG, TC, LDL-C, TAG/HDL-C, TC/HDL-C, LDL-C/HDL-C and non-HDL-C/HDL-C ratio respectively. Moreover, higher asprosin levels was positively associated with newborn BW, BL, HC and CC; however, these associations were not statistically significant.

Conclusion
Overall, our findings support the positive association between cord asprosin concentration and the development of atherogenic lipid profile in newborns. Further studies are needed to confirm the findings of this study in other populations.
RNA-Seq analysis of duck embryo fibroblast cells gene expression during duck Tembusu virus infection
Authors: Pan Yuhong , Wu Xuedong , Cai Wenjun , Cheng Anchun , Wang Mingshu , Chen Shun , Huang Juan , Yang Qiao , Wu Ying , Sun Di , Mao Sai , Zhu Dekang , Liu Mafeng , Zhao Xinxin , Zhang Shaqiu , Gao Qun , Ou Xumin , Tian Bin , Yin Zhongqiong , Jia Renyong 
Published: May 2022

AbstractDuck Tembusu virus (DTMUV), a member of the family Flaviviridae and an economically important pathogen with a broad host range, leads to markedly decreased egg production. However, the molecular mechanism underlying the host-DTMUV interaction remains unclear. Here, we performed high-throughput RNA sequencing (RNA-Seq) to study the dynamic changes in host gene expression at 12, 24, 36, 48 and 60 h post-infection (hpi) in duck embryo fibroblasts (DEF) infected with DTMUV. A total of 3129 differentially expressed genes (DEG) were identified after DTMUV infection. Gene Ontology (GO) category and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these DEG were associated with multiple biological functions, including signal transduction, host immunity, virus infection, cell apoptosis, cell proliferation, and pathogenicity-related and metabolic process signaling pathways. This study analyzed viral infection and host immunity induced by DTMUV infection from a novel perspective, and the results provide valuable information regarding the mechanisms underlying host-DTMUV interactions, which will prove useful for the future development of antiviral drugs or vaccines for poultry, thus benefiting the entire poultry industry.
Single cell transcriptomic analysis of human amnion identifies cell-specific signatures associated with membrane rupture and parturition
Authors: Wang Wang-Sheng , Lin Yi-Kai , Zhang Fan , Lei Wen-Jia , Pan Fang , Zhu Ya-Nan , Lu Jiang-Wen , Zhang Chu-Yue , Zhou Qiong , Ying Hao , Sun Kang 
Published: May 2022

Abstract
Background
The human amnion is an intrauterine tissue which is involved in the initiation of parturition. In-depth understanding of gene expression signatures of individual cell types in the amnion with respect to membrane rupture at parturition may help identify crucial initiators of parturition for the development of specific strategies to prevent preterm birth, a leading cause of perinatal mortality.

Results
Six major cell types were revealed in human amnion including epithelial cells, fibroblasts and immunocytes as well as three other cell types expressing dual cell markers including epithelial/fibroblast, immune/epithelial and immune/fibroblast markers. The existence of cell types expressing these dual cell markers indicates the presence of epithelial-mesenchymal (EMT), epithelial-immune (EIT) and mesenchymal-immune (MIT) transitions in amnion at parturition. We found that the rupture zone of amnion exhibited some specific increases in subcluster proportions of immune and EMT cells related to extracellular matrix remodeling and inflammation in labor. The non-rupture zone exhibited some common changes in subcluster compositions of epithelial and fibroblast cells with the rupture zone in labor, particularly those related to oxidative stress and apoptosis in epithelial cells and zinc ion transport in fibroblasts. Moreover, we identified that C–C motif chemokine ligand 20 (CCL20) was among the top up-regulated genes in amnion epithelial cells, fibroblasts and immunocytes in the rupture zone at parturition. Studies in pregnant mice showed that administration of CCL20 induced immunocytes infiltration to tissues at the maternal–fetal interface and led to preterm birth.

Conclusions
Apart from the conventional epithelial, fibroblast and immunocytes, human amnion cells may undergo EMT, EIT and FIT in preparation for parturition. Intense inflammation and ECM remodeling are present in the rupture zone, while enhanced apoptosis and oxidative stress in epithelial cells and zinc ion transport in fibroblasts are present in amnion regardless of the rupture zones at parturition. CCL20 derived from the major cell types of the amnion participates in labor onset.
The long-term impact of immediate verbal feedback of hand hygiene compliance after overt observation sessions, as assessed by continuous closed-circuit television monitoring in an intensive care setting
Authors: Livshiz-Riven Ilana , Azulay Hovav , Koyfman Leonid , Gushanski Alex , Askira Seada , Abar Vered Ischa , Gruenbaum Benjamin F. , Ivanov Evgenia , Klein Moti , Danziger Asaf , Nativ Ronit , Borer Abraham , Ziv-Baran Tomer , Brotfain Evgeni 
Published: May 2022

Abstract
Background
Hand hygiene compliance by health care workers (HCWs) is pivotal in controlling and preventing health care associated infections. The aim of this interventional study is to assess the long-term impact of personal verbal feedback on hand hygiene compliance of HCWs in an intensive care unit (ICU) immediately after overt observation by an infection control nurse.

Methods
An infection control nurse overtly observed HCWs’ hand hygiene compliance and immediately gave personal verbal feedback with emphasis on aseptic technique. Overt non-interventional sessions were also performed. We measured compliance rates using covert continuous closed-circuit television (CCTV) monitoring. We compared these rates to previously-published hand hygiene compliance data.

Results
Overall compliance rates in the first (41.5%) and third phases (42%) of the study, before and after the intervention were similar. The two moments that were lowest in the first phase, “before aseptic contact” and “after exposure to body fluids”, showed significant improvement, but two moments showed a significant decline in compliance: “before patient contact” and “after contact with patient surrounding”. The compliance rates during the intervention phase were 64.8% and 63.8% during the sessions with and without immediate verbal personal feedback, respectively.

Conclusion
The overall hand hygiene compliance rate of HCWs did not show an improvement after immediate verbal personal feedback. Covert CCTV observational sessions yielded much lower hand hygiene compliance rates then overt interventional and non-interventional observations. We suggest that a single intervention of personal feedback immediately after an observational session is an ineffective strategy to change habitual practices.
Reliability of measuring constructs in applied linguistics research: a comparative study of domestic and international graduate theses
Authors: Razavipour Kioumars , Raji Behnaz 
Published: May 2022

AbstractThe credibility of conclusions arrived at in quantitative research depends, to a large extent, on the quality of data collection instruments used to quantify language and non-language constructs. Despite this, research into data collection instruments used in Applied Linguistics and particularly in the thesis genre remains limited. This study examined the reported reliability of 211 quantitative instruments used in two samples of domestic and international theses in Applied Linguistics. The following qualities in measuring instruments were used to code the data: the instrument origin, instrument reliability, reliability facets examined, reliability computation procedures utilized, and the source of reliability reported (i.e., primary or cited). It was found that information about instrument origin was provided in the majority of cases. However, for 93 instruments, no reliability index was reported and this held true for the measurement of both language and non-language constructs. Further, the most frequently examined facet of reliability was internal consistency estimated via Cronbach’s alpha. In most cases, primary reliability for the actual data was reported. Finally, reliability was more frequently reported in the domestic corpus than in the international corpus. Findings are discussed in light of discursive and sociomaterial considerations and a few implications are suggested.
Regulating the electronic structures of mixed B-site pyrochlore to enhance the turnover frequency in water oxidation
Authors: Zhang Cheng , Wang Fangfang , Xiong Beichen , Yang Hong 
Published: May 2022

AbstractThis paper describes the development of mixed B-site pyrochlore Y2MnRuO7 electrocatalyst for oxygen evolution reaction (OER) in acidic media, a challenge for the development of low-temperature electrolyzer for green hydrogen production. Recently, several theories have been developed to understand the reaction mechanism for OER, though there is an uncertainty in most of the cases, due to the complex surface structures. Several key factors such as lattice oxygen, defect, electronic structure, oxidation state, hydroxyl group and conductivity were identified and shown to be important to the OER activity. The contribution of each factor to the performance however is often not well understood, limiting their impact in guiding the design of OER electrocatalysts. In this work, we showed mixed B-site pyrochlore Y2MnRuO7 catalyst exhibits 14 times higher turnover frequency (TOF) than RuO2 while maintaining a low overpotential of ~ 300 mV for the entire testing period of 24 h in acidic electrolyte. X-ray photoelectron spectroscopy (XPS) analysis reveals that this B-site mixed pyrochlore Y2MnRuO7 has a higher oxidation state of Ru than those of Y2Ru2O7, which could be crucial for improving OER performance as the broadened and lowered Ru 4d band resulted from the B-site substitution by Mn is beneficial to the OER kinetics.
The Y plane is a reliable CT-based reference for glenoid component positioning in shoulder arthroplasty
Authors: Glasson Jean-Marc , van Rooij Floris , Nover Luca , Saffarini Mo , Kany Jean 
Published: May 2022

Abstract
Purpose
To determine the reliability of anatomic references for mediolateral component positioning in shoulder arthroplasty.

Materials and methods
The computed tomography scans of 86 shoulders free of arthritic or anatomic deformities were studied. Two surgeons independently digitized a series of points, including the intersection of the 3 bone branches of the scapular spine (Y), the center of the glenoid surface (G), the most medial point of the scapula (MS), the cortical convergence (CC) of the anterior and posterior margins of the glenoid, the base of the coracoid (BC), the anterior (HA) and posterior (HP) margins of the subchondral bone.

Results
The mean mediolateral distances between G and Y, BC, CC were respectively − 19.6 mm, − 1.5 mm, and − 36.8 mm. The consistency of anatomic landmarks was greatest for Y (standard deviation (SD) =2.3 mm; interquartile range (IQR) =3 mm), compared to BC (SD = 4.6 mm; IQR = 7 mm), and CC (SD = 6.6 mm; IQR = 8 mm). The repeatability of anatomic landmarks was excellent for all measurements. The mean ratios (relative to humeral head size) of distances between G and Y, BC, CC were respectively − 0.45, − 0.04, and − 0.85. The consistency of ratios was greatest for Y (SD = 0.05; IQR = 0.06), compared to BC (SD = 0.11; IQR = 0.14), and CC (SD = 0.13; IQR = 0.17). The repeatability of ratios was excellent for Y and BC, while it was good for CC.

Conclusions
The Y-plane is a reliable reference for glenoid component positioning in shoulder arthroplasty, with a consistent distance from the center of the glenoid surface, and could therefore be suitable for preoperative planning.

Study design
Level III, comparative anatomic study.
Modified Lemaire tenodesis reduces anterior cruciate ligament graft forces during internal tibial torque loading
Authors: Mayr Raul , Sigloch Maximilian , Coppola Christian , Hoermann Romed , Iltchev Alessandra , Schmoelz Werner 
Published: May 2022

AbstractPurposeThe aim of the study was to directly measure graft forces of an anterior cruciate ligament reconstruction (ACLR) and a lateral extra-articular tenodesis (LET) using the modified Lemaire technique in combined anterior cruciate ligament (ACL) deficient and anterolateral rotatory instable knees and to analyse the changes in knee joint motion resulting from combined ACLR + LET.MethodsOn a knee joint test bench, six fresh-frozen cadaveric specimens were tested at 0°, 30°, 60°, and 90° of knee flexion in the following states: 1) intact; 2) with resected ACL; 3) with resected ACL combined with anterolateral rotatory instability; 4) with an isolated ACLR; and 5) with combined ACLR + LET. The specimens were examined under various external loads: 1) unloaded; 2) with an anterior tibial translation force (ATF) of 98 N; 3) with an internal tibial torque (IT) of 5 Nm; and 4) with a combined internal tibial torque of 5 Nm and an anterior tibial translation force of 98 N (IT + ATF). The graft forces of the ACLR and LET were recorded by load cells incorporated into custom devices, which were screwed into the femoral tunnels. Motion of the knee joint was analysed using a 3D camera system.ResultsDuring IT and IT + ATF, the addition of a LET reduced the ACLR graft forces up to 61% between 0° and 60° of flexion (P = 0.028). During IT + ATF, the LET graft forces reached 112 N. ACLR alone did not restore native internal tibial rotation after combined ACL deficiency and anterolateral rotatory instability. Combined ACLR + LET was able to restore native internal tibial rotation values for 0°, 60° and 90° of knee flexion with decreased internal tibial rotation at 30° of flexion.ConclusionThe study demonstrates that the addition of a LET decreases the forces seen by the ACLR graft and reduces residual rotational laxity after isolated ACLR during internal tibial torque loading. Due to load sharing, a LET could support the ACLR graft and perhaps be the reason for reduced repeat rupture rates seen in clinical studies. Care must be taken not to limit the internal tibial rotation when performing a LET.