bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunogenicity and reactogenicity of heterologous Ad26.COV.2 and BNT162b2 vaccination
Authors: Sester Martina , Klemis Verena , Venhorst Andreas , Halmans Lea , Schmidt Tina , Greiß Franziska , Sester Urban , Gärtner Barbara , Meyer Tim 
Published: November 2021

Abstract
Given increased rates of breakthrough infection, German and other national authorities recommend heterologous booster vaccinations for Ad26.COV.2 vaccinated individuals, although data on immunogenicity and reactogenicity are lacking. We therefore recruited fifteen individuals who received the Ad26.COV.2 vaccination followed by a heterologous booster vaccination using the mRNA-vaccine BNT162b2. Immune response included SARS-CoV-2 spike-specific IgG, neutralizing activity as well as Spike-specific CD4 and CD8 T cells. Reactogenicity was self-reported using a questionnaire. We show that induction of specific immunity was poor after one dose of Ad26.COV.2. Heterologous boosting with BNT162b2 led to a significant increase in spike-specific IgG, neutralizing antibodies and CD4 and CD8 T cells. Heterologous boosting was well tolerated with more frequent systemic adverse events after the first dose. Thus, our data support current recommendations for heterologous booster-vaccination to optimize specific immunity and protection against SARS-CoV-2 infection in Ad26.COV.2-vaccinated individuals.
Identification of cross-talk between m6A/m5C regulators and ferroptosis associated with immune infiltration and prognosis in pan-cancer
Authors: Zhang Yingli 
Published: November 2021

Abstract
Although it has been recognized that m6A/5mC methylation and ferroptosis play critical roles in different types of cancers, little is known about the relationship between them. In addition, there is also a growing appreciation that m6A/5mC methylation and ferroptosis may affect immune cell infiltration and activation. This study aimed to reveal the extensive cross-talk between epigenetic modification and ferroptosis. A total of 31 cancer type-specific datasets in TCGA were individually collected by the publicly available web servers for multiple bioinformatic analyses of m6A/5mC regulators and ferroptosis-related genes. Intriguingly, m6A/5mC regulators and ferroptosis-related genes were identified to have considerable global coverage and prognostic significance across multiple cancer types. Moreover, m6A/5mC regulators showed interactive potential with ferroptosis-related genes, and genomic alteration of ferroptosis-related genes coupled with m6A/5mC regulators, at least in pancreatic cancer. Furthermore, m6A/5mC regulators and ferroptosis-related genes were found to be significantly associated with TILs. Finally, m6A/5mC regulators and ferroptosis-related genes exhibited functionally related to each other or co-regulated by TF or non-coding RNA. Together, m6A/5mC methylation and ferroptosis show a wide-ranging connection, and a combination strategy of epigenetic and ferroptosis therapies with ICP inhibitors may benefit more cancer patients in the future.
Living in Patchy Habitats: Substrate Selection for Basking by Sympatric Lizards in Contrasted Anthropogenic Habitats in Western France
Authors: Meek Roger , Luiselli Luca 
Published: November 2021

Abstract
The influence of temperature on the physiological processes in reptiles is well known, for example growth, reproduction, muscular energy are all largely temperature dependent and therefore temperature is a key aspect of reptilian ecology. However, there may be constraints on the ability of reptiles to harness thermal energy, particularly during cold seasons in the temperate zones. Substrate selection is a key aspect in thermoregulation and can enhance heat uptake. For example, wood substrates are known to increase rates of heat gain in basking reptiles enabling earlier attainment of optimum body temperatures compared to other substrate types, which enables increased time available for other activities. In this paper we describe substrate use for basking in two species of lizard, Lacerta bilineata and Podarcis muralis in a hedgerow and suburban garden in western France compared against a null model of substrate availability. When different substrates were pooled based on their material similarities both species were recorded in greater frequency on wood based materials in comparison to their availability compared to non-wood substrates. However at a finer level, in comparison to substrate availability (fallen tree branches, tree stumps, open ground etc), P. muralis showed strong substrate selection for basking, whereas L. bilineata did not depart significantly from the null model. We speculated that intra-specific aggression in L. bilineata was a possible cause of this result due to dominant individuals limiting smaller or female lizards from accessing prime basking sites. Differences in communal basking between the two species supported this notion.
Embeddings from protein language models predict conservation and variant effects
Authors: Marquet Céline , Heinzinger Michael , Olenyi Tobias , Dallago Christian , Bernhofer Michael , Erckert Kyra , Nechaev Dmitrii , Rost Burkhard 
Published: November 2021

Abstract
The emergence of SARS-CoV-2 variants stressed the demand for tools allowing to interpret the effect of single amino acid variants (SAVs) on protein function. While Deep Mutational Scanning (DMS) sets continue to expand our understanding of the mutational landscape of single proteins, the results continue to challenge analyses. Protein Language Models (pLMs) use the latest deep learning (DL) algorithms to leverage growing databases of protein sequences. These methods learn to predict missing or masked amino acids from the context of entire sequence regions. Here, we used pLM representations (embeddings) to predict sequence conservation and SAV effects without multiple sequence alignments (MSAs). Embeddings alone predicted residue conservation almost as accurately from single sequences as ConSeq using MSAs (two-state Matthew Correlation Coefficient – MCC - for ProtT5 embeddings of 0.596 ± 0.006 vs. 0.608 ± 0.006 for ConSeq). Inputting the conservation prediction along with BLOSUM62 substitution scores and pLM mask reconstruction probabilities into a simplistic logistic regression (LR) ensemble for Variant Effect Scoring without alignments (VESPA) predicted SAV effect magnitude without any optimization on DMS data. Comparing predictions for a standard set of 39 DMS experiments to other methods (incl. ESM-1v, DeepSequence, and GEMME) revealed our approach as competitive with the state-of-the-art (SOTA) methods using MSA input. No method outperformed all others, neither consistently nor in a statistically significant manner, independently of the performance measure applied (incl. two-state accuracy: Q2, MCC, Spearman and Pearson correlation). Lastly, we investigated binary effect predictions on DMS experiments for four human proteins. Overall, embedding-based methods have become competitive with methods relying on MSAs for SAV effect prediction at a fraction of the costs in computing/energy. Our method predicted SAV effects for the entire human proteome (~ 20k proteins) within 40 minutes on one Nvidia Quadro RTX 8000. All methods and data sets are freely available for local and online execution through bioembeddings.com, https://github.com/Rostlab/VESPA, and PredictProtein.
Molecular Epidemiology, Risk Factors and Outcomes of Carbapenem-Resistant Klebsiella Pneumoniae Infection in a Tertiary Hospital of Eastern China: For a Retrospective Study Over 4 Years
Authors: Zhao Dongmei , Li Hongru , Yue Chengcheng , Liu Yanyan , Ye Ying , Li Jiabin 
Published: November 2021

Abstract
Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) have undergone extensive dissemination in worldwide resulting in increased mortality. We performed a retrospective analysis of epidemiology and risk factors for the outcome of CRKP infection in a general teaching hospital in China.
Methods

A molecular and clinical study were conducted for 98 CRKP in a tertiary hospital from January 2013 to December 2016. Carbapenemase gene detection, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed. Logistic regression was also used to identify the risk factors associating with the 30-day mortality.
Results

The producition of KPC cabapenemase was the main resistant mechanism and increased annually with a significant difference. However, the molecular outcome revealed the dominance and diversity in CRKP with 24 sequence types (STs) and 59 PFGE types (PTs ). The ST11 CRKP were documented as the predominant strains in our study, which showed a significant increasing trend year by year. Additionally, the predominant ST11 CRKP corresponding to PT10 and PT15 remained a typical fashion. Of note, the new advantage PT09 or PT16 were just discovered in 2016 which also corresponding to ST11. Meanwhile, the factors on 30-day mortality and ST11 proportionality with CRKP infection were assessed, which showed that ST11, appropriate empirical treatment, and hospital stays were independently associated with 30-day mortality.
Conclusions

ST11 CRKP payed a dominant role in the process, but the homology of these strains was polymorphic and the advantage clusters would be changed by evolution. Additionally, besides appropriate empirical treatment and hospital stays, ST11 CRKP was independently associated with the 30-day mortality, first reported as we know.
Interferences of Inorganic Arsenic (III &amp; V) on Growth and Development of Rice (Oryza sativa L.) With Special Emphasis on Root and Coleoptile Growth
Authors: Mondal N.K. , Debnath Priyanka , Mishra Debojyoti 
Published: November 2021

Abstract
A short-term phytotoxicity experiment was conducted on four varieties of rice (Oryza sativa L.) under the influence of arsenic (III & V) to evaluate the impact on root and coleoptiles growth. Four varieties (GB-1, IET-4786, IET-4094, and MTU-1010) of rice were undertaken for this study with different concentrations (0, 5, 10, 25 and 50 mg/L) of arsenic (III & V). Germination along with mean daily germination (MDG), length of root and coleoptile, water holding capacity of root and coleoptiles, fresh and dry weight, arsenic accumulation, MDA and root ion leakage were evaluated. Results highlighted that the percent germination of IET-4094 and MTU-1010 varieties of rice seed over control decreased significantly (p < 0.05) with increasing concentration of both arsenite and arsenate. However, the percent germination of GB-I and IET-4786 dose not affected on the different concentration of both arsenate and arsenite. The root and coleoptile length of all the four varieties showed remarkable decreasing trend over control with increasing concentration of both arsenite and arsenate. However, more pronounced effects were observed for arsenite than arsenate. Similarly, biomass of shoot is less affected than root under different concentration of arsenite and arsenate. The variety IET-4786 and MTU-1010, accumulated lower level of arsenic and variety GB-1 accumulate higher level of MDA level in root under both arsenite and arsenate treatments. Therefore, it can be concluded that the variety IET-4786 and MTU-1010 are the suitable varieties towards phytoremediation of both arsenite and arsenate. Moreover, farmers of arsenic contaminated area are recommended to cultivate IET-4786 and MTU-1010 varieties.
Identification of Patients Requiring Adrenalectomy for Unilateral Adrenal Tumors Through a Dual Approach: ceCT and [18F]FDG-PET
Authors: Farolfi Andrea , Maietti Elisa , Piperno Federica , Coppolino Pietro , Dalmazi Guido Di , Zavatta Guido , De Leo Antonio , Cintio Ilaria Di , Fanti Stefano , Golfieri Rita , Lambertini Alessandro , Malandra Jennifer , Mosconi Cristina , Pagotto Uberto , Santini Donatella , Selva Saverio , Vicennati Valentina , Nanni Cristina 
Published: November 2021

Abstract
PurposeHormonal assessment (HA) and contrast-enhanced CT (ceCT) show insufficient sensitivity and specificity when staging unilateral adrenal lesions (ALs). We aimed at: 1) developing an imaging-based, i.e. ceCT and FDG-PET, diagnostic score able to discriminate adrenal tumors entailing adrenalectomy from those who need clinical monitoring, and 2) identifying a diagnostic flow-chart that allows clinicians to avoid unneeded diagnostic procedures and to address patients to the optimal management.MethodsRetrospective single-center study assessing patients with unilateral AL and the following inclusion criteria: a) a four-phase ceCT; b) FDG-PET within one month of the ceCT; c) histopathology or a clinical follow-up of at least 24 months. Firstly, multivariate logistic regression analysis was employed to identify the predictors of adrenal tumors to treat surgically (AL-to-treat) and regression-based coefficients were used to develop a diagnostic score. Secondly, using cut-offs of predictor variables, a diagnostic flow-chart was defined.ResultsForty-eight patients were enrolled (mean age 61 years), of whom 21/48 (44%) had AL-to-treat. The remaining 27/48 (56%) presented with AL to follow-up only (i.e. benign). Maximum and minimum lesion diameter, Hounsfield units (HU) before contrast media injection and HU at the delayed phase (HUdelayed), relative and absolute washout, AL SUVmax, AL SUVmean, ratio SUVmax AL/SUVmax liver (adrenal-liver ratio) were associated with the presence of AL-to-treat (all p<0.05). In multiple logistic regression analysis, SUVmax and HUdelayed showed to be significant predictors of AL-to-treat and were used to create a diagnostic score. ceCT parameters’ cut-offs discriminating AL-to-treat surgically from AL-to-follow-up with 100% PPV and NPV were first identified, finding 4/48 AL-to-treat and 15/48 ALs to follow-up. Applying the adrenal-liver ratio cut-off of 1.7 to the 29/48 remaining patients with uncertain AL management, for adrenal tumors we found an overall accuracy, sensitivity and specificity of 83%, 76% and 89%, respectively, and a diagnostic flow-chart based on these results was proposed. ConclusionWe developed a two-parameter imaging-based score that may be applied to predict adrenal tumors requiring adrenalectomy. Furthermore, a diagnostic flow-chart to stratify patients on the basis of the optimal management was proposed, thus guiding undefined unilateral adrenal lesions to FDG-PET imaging.
ConTEXT: Context-aware Adaptive SMS Client for Drivers to Reduce Risky Driving Behaviors
Authors: Khan Inayat , Khusro Shah 
Published: November 2021

Abstract
Text messaging while driving has been considered a dangerous activity that may lead to serious injuries and traffic fatalities. Several assistive technologies and solutions have been developed to simplify texting activity. However, due to inconsistent and complex interface design, lack of logical navigational order, lack of context, complicated text-entry layouts, and laborious activities, the existing texting-related activities can lead to accidents. This paper recognized the risky driving patterns using the real-time AutoLog application. Based on this risky driving behavior, we have proposed ConTEXT, a usable SMS client, to overcome the issues pertaining to the usability of textual activities on smartphones while driving. ConTEXT application is evaluated both empirically as well as through real-time AutoLog application. We have collected data from 117 drivers through a questionnaire. The results show that the data is found reliable also alpha scores for all factors seem internally consistent as it ranges from 0.70 to 0.79 which is good. Similarly, we have reported Principal Component Factor Analysis (PCFA), which was found satisfied and appropriate as the Eigenvalue for all the factors is greater than zero. Furthermore, results obtained from the AutoLog dataset show an improved user experience, better control over the touch screen with minimum visual, physical, and mental load.
Adaptive foraging behaviour increases vulnerability to climate change
Authors: Gauzens Benoit , Rosenbaum Benjamin , Kalinkat Gregor , Boy Thomas , Jochum Malte , Kortsch Susanne , O'Gorman Eoin , Brose Ulrich 
Published: November 2021

Abstract
Adaptative foraging behavior should promote species coexistence and biodiversity under climate change as predators are expected to maximize their energy intake, according to principles of optimal foraging theory. We test these assumptions using a dataset comprising 22,185 stomach contents of fish species across functional groups, feeding strategies, and prey availability in the environment over 12 years. Our results show that foraging shifts from trait-dependent prey selectivity to density dependence in warmer and more productive environments. This behavioral change leads to lower consumption efficiency as species shift away from their optimal trophic niche, undermining species persistence and biodiversity. By integrating this adaptive foraging behavior into dynamic models, our study reveals higher risk profiles for ecosystems under global warming.
Fused Second-Order MR Image Feature Framework for Region of Interest Delineation
Authors: Banday Shoaib Amin , Khan Samiya , Mir A. H. 
Published: November 2021

Abstract
Healthcare infrastructure relies on technology-driven solutions such as CAD systems for improving the overall efficiency of its procedures and processes. Image segmentation is one of the most critical phases for such systems in view of the fact that accuracy of this phase determines the efficacy of the later phases, to a large extent. Extensive research is underway to develop segmentation techniques that can achieve highest accuracy with some suggestions directed towards an information fusion based approach within the machine learning paradigm. This research paper proposes a fused second-order statistical image feature framework for Region of Interest delineation. It is a feature fusion-based segmentation approach (ACM-FT) that fuses texture driven feature maps from GLCM , GLRLM and Gabor filters. The proposed approach is then compared with Active Contour Model with classical edge detection method (ACM-ED) and Active Contour Model without edges (ACM-WE) using Overlap Index (OI) and Jackard’s Similarity Co-efficient (JSI). The proposed approach achieves an average accuracy of 92.17% and 93.19% for JSI and OI, respectively, demonstrating significant improvements.
TPX2 Amplification-Driven Aberrant Mitosis in Culture Adapted Human Embryonic Stem Cells With Gain of 20q11.21
Authors: Jeong Ho-Chang , Go Young-Hyun , Shin Joong-Gon , Kim Yun-Jeong , Cho Min-Guk , Gwon Dasom , Cheong Hyun Sub , Lee Haeseung , Lee Jae-Ho , Jang Chang-Young , Shin Hyoung Doo , Cha Hyuk-Jin 
Published: November 2021

Abstract
Despite highly effective machinery for the maintenance of genome integrity in human embryonic stem cells (hESCs), the frequency of genetic aberrations during in-vitro culture has been a serious issue for future clinical applications. By passaging hESCs over a broad range of timepoints, we found that mitotic aberrations, such as the delay of mitosis, multipolar centrosomes, and chromosome mis-segregation, were increased in parallel with polyploidy compared to early-passaged hESCs (EP-hESCs) with normal copy number. Through high-resolution genome-wide approaches and transcriptome analysis, we found that culture adapted-hESCs with a minimal amplicon in chromosome 20q11.21 highly expressed TPX2, a key protein for governing spindle assembly and cancer malignancy. Consistent with these findings, the inducible expression of TPX2 in EP-hESCs reproduced aberrant mitotic events, such as the delay of mitotic progression, spindle stabilization, misaligned chromosomes, and polyploidy, suggesting that the increased transcription of TPX2 in culture adapted hESCs could contribute to an increase in aberrant mitosis due to altered spindle dynamics.
Quality of Life in Young Illicit Substance Abuser Men: Testing a Moderated Mediation Model of Age Related Decline in Executive Functions
Authors: Fatima Shameem , Hassan Sajid , Jamil Farhat 
Published: November 2021

Abstract
Background
Earlier literature has documented age related decline in executive functions (EF) in normal aging adults, yet it is unclear whether age related EF decline is linked with quality of life (QoL) possibly mediating the link between age and QoL. Therefore, the study hypothesized that selective EF components would mediate the association between age and QoL domains in young substance abuser men and family history of substance use would moderate these mediated associations.
Method
A sample of 212 young substance abuser men (105 positive family history and 107 negative family history of substance use) performed on performance measures assessing selective EF components—inhibition and cognitive flexibility. Also, they reported their QoL on self-report measure of WHOQOL.
Results
Mean scores of the sample on all QoL domains were lower than expected by chance. Also, the participants with positive family history of substance use compared to those with negative family history scored significantly lower on all QoL domains except physical QoL. Mediation analyses revealed that of two EF components, only inhibition mediated the negative association of age with psychological, social, and environmental QoL. Furthermore, family history of substance use moderated all the significant mediations with stronger indirect negative associations in participants having a family history of substance use compared to those with no such history.
Conclusion
It is concluded that inhibitory control, which is vulnerable to aging, substance use, and family history of substance use, is an important factor related to QoL in young substance abuser men.
The Role of Network Capabiliity in Shaping Behavior E-commerce Acceptance Among Small Businesses in Keranggan Village
Authors: Yuniarty Yuniarty , Prabowo Hartiwi , Ikhsan Ridho Bramulya 
Published: November 2021

This research is a case study to help identify the driving factors of e-commerce acceptance by small businesses in Keranggan Village in Indonesia. This study argues that factors such as technology-organization-environment need to be strengthened by network capability from business actors so that e-commerce adoption intention emerges. From the total samples of 100 business actors in Keranggan Village. The study utilized Structural Equation Modeling (SEM) with SmartPLS 3.0 for data examination. Consequently, the relationship of technological context with e-commerce acceptance is mediated by significant network capability.
An economic evaluation of teledermatology care delivery for chronic skin diseases
Authors: Skinner Robert , Breck Andrew , Esposito Dominick 
Published: November 2021

Aim:
Analyze the impact of nationwide implementation of teledermatological care for psoriasis.
Methods:
Develop a Markov model that estimates the impact of telehealth technology for treatment of moderate-to-severe psoriasis on health and healthcare expenditures compared with in-person clinical care.
Results:
Lower medical costs by US$1.5 billion and total social costs of US$4.3 billion over 5 years. Patients save more than 67 million hours in work absenteeism and travel time, valued at US$598 million. Employers save US$1.2 billion over 5 years due to decreased employee absenteeism.
Conclusion:
National implementation of telehealth for psoriasis care has the potential to substantially reduce both formal healthcare costs and informal costs for families and patients, while maintaining equivalent clinical outcomes as traditional in-person care.