bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly conserved interaction profiles between clinically relevant mutants of the cytomegalovirus CDK-like kinase pUL97 and human cyclins: functional significance of cyclin H
Authors: Schütz Martin , Müller Regina , Socher Eileen , Wangen Christina , Full Florian , Wyler Emanuel , Wong Diana , Scherer Myriam , Stamminger Thomas , Chou Sunwen , Rawlinson William D. , Hamilton Stuart T. , Sticht Heinrich , Marschall Manfred 
Published: June 2022

Abstract
The complex network of host interaction of the human cytomegalovirus (HCMV) involves the regulatory protein kinase pUL97, which represents a viral cyclin-dependent kinase (CDK) ortholog. pUL97 interacts with the three human cyclin types T1, H and B1, whereby the binding region of cyclin T1 and the pUL97 oligomerization region were both assigned to amino acids 231–280. We further addressed the question whether HCMVs harboring mutations in ORF-UL97, i.e. short deletions or resistance-conferring point mutations, are affected in the interaction with human cyclins and viral replication. To this end, clinically relevant UL97 drug resistance-conferring mutants were analyzed by whole-genome sequencing and used for genetic marker transfer experiments. The recombinant HCMVs indicated conservation of pUL97–cyclin interaction, since all viral UL97 point mutants still showed interaction with the analyzed cyclin types and exerted wild-type-like replication fitness. In comparison, recombinant HCMVs UL97 Δ231–280 and Δ236–275 lost interaction with cyclins T1 and H, showed an impaired replication efficiency and also reduced kinase activity. Moreover, a cellular knock-out of cyclins B1 or T1 did not alter HCMV replication phenotypes or pUL97 kinase activity, possibly indicating alternative, compensatory pUL97–cyclin interactions. To the contrary, however, cyclin H knock-out, similar to virus deletion mutants in the pUL97–cyclin H binding region, exhibited strong defective phenotypes of HCMV replication. Thus, cyclin H proved to be a very relevant determinant of both, pUL97 kinase activity and viral replication efficiency. Combined, the results provide evidence for the functional importance of pUL97–cyclin interaction, and a high selective pressure on the formation of pUL97–cyclin complexes as identified for clinically relevant mutants.
Rapid extraction of toluene from water samples based on CNTs – nitrogen-doped porous graphene nanostructures by packed syringe membrane filter solid-phase microextraction before determination by gas chromatography
Authors: Teimoori Shahnaz , Shirkhanloo hamid , Hassani Amir Hessam , Panahi Mostafa , Mansouri Nabiollah 
Published: June 2022

Abstract
The authors have requested that this preprint be removed from Research Square.
Effects of Receiving Renal Biopsy on the Prognosis of Chronic Kidney Disease Patients with Impaired Renal Function
Authors: Zhang Tianyi , Yang Xiaoqian , Zhang Minfang , Zhou Wenyan , Jin Yan , Zhou Hang , Zhou Yin , Wang Qin , Mou Shan 
Published: June 2022

Abstract
Background: Impaired renal function was not a recognized indication for renal biopsy. The effects of receiving renal biopsy on the renal functional prognosis for chronic kidney disease (CKD) patients with impaired renal function need to be explored.Methods: This study retrospectively enrolled 300 renal function impaired CKD patients in Renji Hospital from January 2015 to December 2017, 150 of them received percutaneous renal biopsy while the others did not. The endpoint was ≥50% estimated glomerular filtration rate (eGFR) decline from baseline or development of end-stage renal disease (ESRD). Kaplan-Meier analysis with log-rank test was performed to compare the renal survival probability between patients receiving renal biopsy or not. Univariate and multivariate analysis with Cox regression were conducted with predictors of poor renal outcomes in the study cohort.Results: The median follow-up period was 37.6 months. During the follow-up period, the eGFR of the biopsy group increased from 52.2±14.4 to 67.4±37.8 ml/min/1.73m², but decreased from 55.3±17.1 to 29.8±19.1 ml/min/1.73m² in the non-biopsy group. Patients who received renal biopsy had significantly higher renal survival probability (P<0.001). Cox regression analysis revealed that 24-hour urine protein excretion (24h UPE) more than 1g/d was an independent predictor for poor renal outcomes in the non-biopsy group but not in the renal biopsy group (HR=1.719, P=0.040). Conclusion: CKD patients with impaired renal function are recommended to receive renal biopsy to make pathological diagnoses, especially for those with the 24-hour urine protein excretion more than 1g/d.
Knowledge, attitude, and practice regarding child maltreatment amongst Iranian medical students through internship course: An 18-month longitudinal study
Authors: Boroon Mahsa , Mokhtari Saba , Nojomi Marzieh , Hadi Fatemeh , Sorayya Shiva , Shalbafan Mohammadreza 
Published: June 2022

Abstract
Background: Child maltreatment or abuse has been a worldwide major problem and has remained a persistent public health challenge in all countries. Physicians have a significant role in the prevention and intervention of child maltreatment. An educated physician that can effectively identify and report child maltreatment, can fill one of the largest gaps in reducing child abuse.This study was performed to examine the knowledge, attitude, and practice regarding child maltreatment amongst Iranian medical students through internship course.Method: All the medical students (235 students) of the Iran University of Medical Sciences who passed the internship entrance exam in 2019-2020 academic year participated in this study. The participants completed the questionnaire about their attitude, knowledge and practice skills in the first month of their internship course and then completed the same questionnaire 18 months later, at the end-point of the internship period.Results: 139 (59.1%) participants were female and 96 (40.9%) were male. The mean age of the subjects was 24.35±0.76. Only 7 (3%) of them formerly received any education about child maltreatment.There was a significant difference in scores of the knowledge of diagnosis (p-value< 0.001), the practice of prevention (p-value< 0.002) and the general subscale of the practice section (p-value< 0.001) during the internship course. However, the performance of participants decreased with a significant difference in the subscales of the attitude towards diagnosis (p-value< 0.001) and the attitude towards reporting (p-value< 0.001).At the end of the study, the result of graduated physicians was: The total knowledge and attitude of participants were satisfactory and the majority of the participants were at good levels. Although, in the practice subscale, 70.6% of the participants didn’t identify, 84.7% didn’t refer, and 86.4% didn’t report a case of child abuse in the past year.Conclusion: The knowledge and attitude of Iranian recently graduated physicians regarding child maltreatment are at a satisfactory level. Although, the practice level has deficiencies and needs more education. In addition, the change of the knowledge, attitude and practice regarding child maltreatment of medical students during internship course is not sufficient and there are multiple obstacles that need to be solved.
Does patient satisfaction after foot surgery change with time? A mid-term retrospective study using PASCOM-10
Authors: North Victoria , Reilly Ian Neil , Brigden Andy 
Published: June 2022

Abstract
Background: Recording patient reported outcome measurements at six months after surgery using PASCOM-10 is common practice in podiatric surgery. The aim of this study is to establish if patient satisfaction after foot surgery is changed at the 12 month point.Method: An audit of patient reported outcomes following foot surgery was undertaken. Electronic case notes were examined, and 236 patients were identified over a 1-year period. Patients completed the Manchester Oxford Foot Questionnaire (MOXFQ) pre-surgery, at six-months post-operatively (in person/telephone conversation) and were then invited by letter to re-complete this again at 12-months post-operatively. 91 participants (39%) completed both post-operative questionnaires (66 females 25 males). The average age was 64 (range: 35-93). Results: The results demonstrate that there was a significant effect between the three time points in the MOXFQ domains of walking/standing, pain and social interaction (0.353, F (6, 356) = 40.59, p <.001), and a further interaction with gender (0.435, F (6,352) = 30.23, p <.001). An average, positive change in patient satisfaction in all domains is the greatest from pre-surgery to 6-months post-surgery at 78% and then decreases to 62% 12-months post-surgery. Negative and insignificant changes are highest from 6 to 12 months. Females experience lower satisfaction at the six- and 12-month post-operative time points but gain the greatest improvement in patient satisfaction at 30%. National PASCOM data significant with all domain comparisons data (p< .001) is a subset. Conclusion: A patient centred approach is key in foot surgery when determining patient satisfaction. Patient satisfaction levels change significantly at different time points. In this review, the overall patient satisfaction improved with surgery, but with a higher response score at six months than 12. A short period of recovery may not yield the genuine long-term patient reported outcomes and increase to 12 months is recommended from the more common six months. However, the differencing methods of collecting post-operative data may have had an influence on scores.
An Efficient Keyword Search on Temporal Graphs
Authors: Ge Youming , Chen Zitong , Liu Yubao 
Published: June 2022

Abstract
Keyword search on temporal graph is to find a tree covering a set of query labels and being valid in the query time interval. It has many applications in cloud computing, community detection, social network, collaborative project, and so on. However, the existing methods are limited in solving the problem of keyword search on temporal graphs. We propose two basic algorithms, the discrete timestamp algorithm, and the approximate algorithm , the idea of which is trying to turn the problem into the traditional keyword search on graph. To address the low efficiency and low quality of the two basic algorithms, we propose a new algorithm based on dynamic programming to solve the keyword search on temporal graph. The idea is to extend a leaf vertex into a solution by edge-growth operation and tree-merger operation. We also propose two powerful pruning techniques to reduce the intermediate results during the extension. To speed up the algorithm further, we show that our algorithms can be easily parallel. Besides, all algorithms we proposed can handle different kinds of ranking functions well, and all of them can be adaptive to top-N keyword querying by simply changing the stop condition. The efficiency and effectiveness of the proposed algorithms are verified through extensive empirical studies.
The impact of alcoholic drinks and dietary factors on epigenetic markers associated with triglyceride levels
Authors: Lai Chao-Qiang , Parnell Laurence , Lee Yu-Chi , Zeng Haihan , Smith Caren , McKeown McKeown Nicola M. , Ordovas Jose 
Published: June 2022

Abstract
Background: Although current evidence shows that environmental and lifestyle factors are associated with DNA methylation patterns, mechanisms underlying the relationship between diet and other exposures and epigenetic profiles remain to be fully described. To clarify the unique connections between dietary intake and lifestyle factors on disease risk, we conducted epigenetic mapping of diet and lifestyle habits for plasma triglyceride concentrations (TG) by investigating links between lifestyle, including diet, and methylation marks with TG. Methods: We first conducted an epigenome-wide association study (EWAS) for TG in the Framingham Heart Study Offspring population (n=2,178). We then examined the relationships between dietary and lifestyle-related variables, collected over 13 years, and differential DNA methylation sites (DMSs) associated with the last TG measures (exam 8). Second, we conducted a mediation analysis to evaluate causal relationships between diet-related variables and TG. Results: The EWAS revealed 28 TG-associated DMSs at 19 regions (e.g., ABCG1, CPT1A, DHCR24, GARS, NCORS, PFKFB3, PHGDH, PPP2R2B, RNF145, SARS, SLC1A5, SLC43A1, SLC7A11 SREBF1, TXNIP, ZFHX3). After accounting for multiple testing, we identified 427 significant associations (representative of 102 unique associations) between these DMSs and one or more dietary and lifestyle-related variables. The most significant and consistent associations between 11 TG-associated DMSs and diet were alcohol and carbohydrate intake (% total energy), with P-values ranging from 2.89E-04 to 8.37E-70. Mediation analyses demonstrated that alcohol and carbohydrate intake independently affect TG via DMSs as mediators. For seven of the 19 identified DMS regions, higher alcohol intake was associated with lower methylation and higher TG. In contrast, increased carbohydrate intake was associated with higher DNA methylation at two epigenetic loci (CPT1A and SLC7A11) and lower TG. Conclusions: Our findings imply that TG-associated DMSs reflect dietary intakes that could affect cardiometabolic disease risk via epigenetic changes, specifically through their impact on DNA methylation.
Effectiveness of developing a self-management mobile app on the quality of life of women with breast cancer: a study in a developing country Running Title :Impact of a self-management app on breast cancer patients' quality of life
Authors: Jebraeily Mohamad , Eghtedar Samereh , Ayatollahi Haleh , Mohammadzadeh Zahra 
Published: June 2022

Abstract
Background: Self-management involves taking responsibility for your own health and taking the initiative to do so. This can be accomplished by learning information and skills that will help you deal with the difficulties you may encounter during and after your cancer treatment. The aim of this study was to develop a self-management mobile app for women with breast cancer and evaluate of in Iran impact it on the quality of life of patients.Method: This study is a methodological study in 2021. We developed the app during three phases. The QLACS questionnaire and Excel software were used to collect and analyze the data. A total of 24 breast cancer patients were included in the study.Result: Among the most significant changes were in the Quality of Life level, highest respectively: social avoidance (pre: 6.41 – post: 3.56), negative feelings (pre: 5.93 - post: 3.40), sexual function (pre: 6.80 - post: 5.04), sexual interest (pre: 6.41 - post: 4.75) and pain (pre: 6.37 - post: 4.97). And least the changes respectively: distress-family (pre: 7 - post: 7), distress-recurrence (pre: 4.49 - post: 4.38), benefits (pre: 2.47 - post: 3.12), appearance (pre: 4.10 - post: 3.32).Conclusion: Breast cancer patients' quality of life can be improved by providing more targeted content through more accessible tools such as mobile apps.
The prokaryotic Gabija complex senses both viral transcription and DNA metabolism for antiviral defense
Authors: Cheng Rui , Huang Fengtao , Lu Xueling , Yan Yan , Yu Bingbing , Wang Xionglue , Zhu Bin 
Published: June 2022

Abstract
The perpetual arms race between bacteria and phages has led to the development of ingenious bacterial defense systems, including an immense array of unknown systems in addition to the well-known restriction-modification and CRISPR/Cas systems, one of the most dominant of which is the Gabija system, which exists in 8.5% of sequenced bacteria and archaea. The Gabija system consists of the GajA and GajB proteins. We revealed that GajA is a DNA nicking endonuclease that senses NTP depletion by phage transcription. The DNA binding of GajA is strictly inhibited by NTP and the antiviral defense of GajA requires the assistance from GajB, which senses DNA termini produced from phage DNA replication and recombination to hydrolyze (d)A/(d)GTP. The GajB gene encodes two colinear forms of proteins. The full-length GajBʹ protein exhibits stronger ATP hydrolysis activity and is sufficient to support bacteriophage resistance. GajA forms tetramers in vitro and tightly binds to GajB and/or GajBʹ to form stable complexes in vivo and in vitro. However, the 1:1 GajA/B or GajA/Bʹ complex has no antiviral activity. To constitute a functional Gabija complex, fine regulation at the protein expression level is required to maintain the molecular ratio between GajB/GajBʹ and GajA below 1:1. Through (i) multiple sensing of phage pivot activities including transcription and DNA replication and recombination and (ii) fine stoichiometry regulation of the DNA processing complex, the Gabija system exhibits a delicate and concise mechanism distinct from any known prokaryotic antiviral system.
Attitude, Control, and the Finiteness Distinction in Chinese
Authors: Liao Wei-wen , Wang Yuyun 
Published: June 2022

Abstract
It is generally assumed that the notion of finiteness is not applicable to Chinese due to the lack of grammatical tense/person agreement. Meanwhile, syntactic evidence suggests that the finiteness distinction can be made from predicate types in Chinese, but exactly how finiteness is defined and why predicate types may determine finiteness in Chinese remain obscure. The paper argues that the paradox of finiteness distinction in Chinese can be solved if we assume a parameterized version of Bianchi’s (2003) definition of finiteness based on logophoric anchoring. Specifically, due to the lack of tense or person agreement, Chinese employs ‘world’ as the primary anchoring device, and since world-anchoring is correlated to the propositional attitude of the matrix predicate, this gives us an explanation why the finiteness of Chinese is sensitive to predicate types. We further argue that infinitive control complements are embedded jussive clauses in Chinese, and the internal world-anchoring is forced by a performative modal element that is present in both jussive and control clauses. By assuming that the embedded control clause is a centered proposition (a set of individual-world pairs) and the performative modal element anchors it to the internal speaker/addressee, the semantic mechanism allows us to unify various proposals regarding control and finiteness.
Empirical Analysis of Normal Selenium Level in Taiwanese
Authors: Khoo Seokkooi , Chao Ting-Yu , Chen Yen-Ling , Chu Yi-Wen , Chien Du-Shieng 
Published: June 2022

Abstract
Selenium (Se) is an essential micromineral that is incorporated into the active center of selenoproteins which play important roles in regulating immune function, thyroid function, antioxidant defense, and glucose homeostasis. Dietary intakes and bodily levels of Se vary across countries due to geographical distribution of the mineral, dietary patterns, Se species, and genetic predispositions. Biomarkers such as serum/plasma Se, tissue Se, and bioactivity of selenoproteins to suggest Se status of an individual have been proposed and used in epidemiological and clinical studies. Beside vulnerable populations residing in Se-deficient regions, Se deficiency is found in patients of chronic illness, cancer, and those experiencing severe trauma; Se supplementation to this group has been shown to provide benefits including reduced mortality rates and better prognosis. However, there is a lack of consensus to determine Se adequacy and deficiency in terms of health and disease in the context of the local Taiwanese population. In this study, plasma and serum Se values reported from selected studies were pooled to calculate the normal Se range of the general adult Taiwanese. The calculated mean ± standard deviation values of Se level were 182.8 ± 124.3 μg/L (N = 5,508), and the range of Se levels was estimated to be approximately 58–307 mg/L. From this range, Se < 98.8 mg/L was suggestive of deficiency and required Se supplementation, whereas maintaining adequate levels of Se in the range of 125–183 mg/L would help to optimize its role in physiological well-being and disease prevention in Taiwanese adults.
Compatible director fields in $\mathbb{R}^3$
Authors: Silva Luiz C. B. da , Bar Tal , Efrati Efi 
Published: June 2022

Abstract
The geometry and interactions between the constituents of a liquid crystal, which are responsible for inducing the partial order in the fluid, may locally favor an attempted phase that could not be realized in $\mathbb{R}^3$. While states that are incompatible with the geometry of $\mathbb{R}^3$ were identified more than 50 years ago, the collection of compatible states remained poorly understood and not well characterized. Recently, the compatibility conditions for three-dimensional director fields were derived using the method of moving frames. These compatibility conditions take the form of six differential relations in five scalar fields locally characterizing the director field. In this work, we rederive these equations using a more transparent approach employing vector calculus and characterize a wide collection of compatible phases.
An immune signature for risk stratification and therapeutic prediction in helicobacter pylori-infected gastric cancer
Authors: Geng haigang , Dong Zhongyi , Zhang Linmeng , Yang Chen , Li Tingting , Lin Yuxuan , Ke Shouyu , Xia Xiang , Zhang Zizhen , Zhao Gang , Zhu Chunchao 
Published: June 2022

Abstract
Helicobacter pylori (HP) infection is the greatest risk factor for gastric cancer (GC). Increasing evidence has clarified that tumor immune microenvironment (TIME) is closely related to the prognosis and therapeutic efficacy of HP-positive (HP+) GC patients. In this study, we aimed to construct a novel immune-related signature for predicting the prognosis and immunotherapy efficacy of HP + GC patients. A total of 153 HP + GC from three different cohorts were included in this study. An Immune-Related prognostic Signature for HP + GC patients (IRSHG) was established using Univariate Cox regression, the LASSO algorithm, and Multivariate Cox regression. Univariate and Multivariate analyses proved IRSHG was an independent prognostic predictor for HP + GC patients, and an IRSHG-integrated nomogram was established to quantitatively access the prognostic risk. The low-IRSHG group exhibited higher copy number load and distinct mutation profiles compared with the high-IRSHG group. In addition, the difference of hallmark pathways and immune cells infiltration between the two groups was investigated. Notably, tumor immune dysfunction and exclusion (TIDE) analysis indicated that the low-IRSHG group had a higher sensitivity to anti-PD-1 immunotherapy, which was validated by an external pabolizumab treatment cohort. Besides, 98 chemotherapeutic drugs and corresponding potential biomarkers were identified for two groups, and several drugs with potential ability to reverse IRSHG score were identified using CMap analysis. Collectively, IRSHG may serve as a promising biomarker for survival outcome as well as immunotherapy efficacy. Furthermore, it can also help to prioritize potential therapeutics for HP + GC patients, providing new insight for the personalized treatment of HP-infected GC.