bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data-driven discovery of targets for bipotent anticancer drugs identifies Estrogen Related Receptor Alpha
Authors: Sahu Avinash D. , Wang Xiaoman , Munson Phillip , Klomp Jan , Wang Xiaoqing , Gu Shengqing , Qian Gege , Nicol Phillip , Zeng Zexian , Wang Chenfei , Tokheim Collin , Zhang Wubing , Fu Jingxin , Wang Jin , Nair Nishanth U. , Rens Joost , Bourajjaj Meriem , Jansen Bas , Leenders Inge , Lemmers Jaap , Musters Mark , Zanten Sanne van , Zelst Laura van , Worthington Jenny , Brown Myles , Liu Jun S. , Juric Dejan , Meyer Cliff A. , Oubrie Arthur , Liu X. Shirley , Fisher David E. , Flaherty Keith T. 
Published: October 2021

AbstractDrugs that kill tumors through multiple mechanisms have potential for broad clinical benefits, with a reduced propensity to resistance. We developed BipotentR, a computational approach to find cancer-cell-specific regulators that simultaneously modulate tumor immunity and another oncogenic pathway. Using tumor metabolism as proof-of-principle, BipotentR identified 38 candidate immune-metabolic regulators by combining epigenomes with bulk and single-cell tumor transcriptomes from patients. Inhibition of top candidate ESRRA (Estrogen Related Receptor Alpha) killed tumors by direct effects on energy metabolism and two immune mechanisms: (i) cytokine induction, causing proinflammatory macrophage polarization (ii) antigen-presentation stimulation, recruiting CD8+T cells into tumors. ESRRA is activated in immune-suppressive and immunotherapy-resistant tumors of many types, suggesting broad clinical relevance. We also applied BipotentR to angiogenesis and growth-suppressor pathways, demonstrating a widely applicable approach to identify drug targets that act simultaneously through multiple mechanisms. BipotentR is publicly available at http://bipotentr.dfci.harvard.edu/.One-Sentence SummaryBipotentR identifies targets for bipotent anticancer drugs, as shown by the energy and immune effects of ESRRA inhibition.
Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch
Authors: Cheng Luyi , White Elise N. , Brandt Naomi L. , Yu Angela M , Chen Alan A. , Lucks Julius B. 
Published: October 2021

ABSTRACTRNA folds cotranscriptionally to traverse out-of-equilibrium intermediate structures that are important for RNA function in the context of gene regulation. To investigate this process, here we study the structure and function of the Bacillus subtilis yxjA purine riboswitch, a transcriptional riboswitch that downregulates a nucleoside transporter in response to binding guanine. Although the aptamer and expression platform domain sequences of the yxjA riboswitch do not completely overlap, we hypothesized that a strand exchange process triggers its structural switching in response to ligand binding. In vivo fluorescence assays, structural chemical probing data, and experimentally informed secondary structure modeling suggest the presence of a nascent intermediate central helix. The formation of this central helix in the absence of ligand appears to compete with both the aptamer’s P1 helix and the expression platform’s transcriptional terminator. All-atom molecular dynamics simulations support the hypothesis that ligand binding stabilizes the aptamer P1 helix against central helix strand invasion, thus allowing the terminator to form. These results present a potential model mechanism to explain how ligand binding can induce downstream conformational changes by influencing local strand displacement processes of intermediate folds that could be at play in multiple riboswitch classes.
Differential momentary reports of stress and affect associated with alcohol consumption in middle-aged versus younger adults
Authors: Peterson Hope , Rejeski W. Jack , Fanning Jason , Porges Stephen W. , Heilman Keri J. , Laurienti Paul J. , Gauvin Lise 
Published: October 2021

AbstractObjectiveStress is a motivator to consume alcohol, a well-documented relapse risk, and is known to differentially affect biological and psychological processes as people age. Because alcohol consumption is known to decrease stress and increase affect, this study examined differences in ratings of stress and affect across the day in middle-aged versus younger adults who regularly consumed alcohol.MethodsA sample of males and females including younger (n=17) and middle-aged (n=18) drinkers was studied across two experimental periods: a 3-day period of usual drinking and a 3-day period of abstinence from alcohol. We also measured resting levels of respiratory sinus arrhythmia (RSArest), since it is a well-documented biomarker of stress and known to decrease with age. Ecological momentary assessment (EMA) ratings across periods of normal drinking and abstinence were modeled using hierarchical regression to assess differences in stress and affect throughout days of abstinence and normal drinking between the two age groups.ResultsAs anticipated, middle-aged participants had lower RSArest than those who were younger. Our analyses showed that middle-aged adults experienced a significant reduction in stress following drinking while no such effect was observed in the younger adults. Although the middle-aged adults showed overall lower stress, generally they also expressed higher affect than younger adults.ConclusionsDespite the mitigating role of alcohol on stress in the middle-aged group and the fact that they had higher affect than the younger adults, their lower levels of RSArest and higher daily reports of stress could pose a risk for chronic alcohol consumption.
Linear indexing for all strings under all internal nodes in suffix trees
Authors: Al-okaily Anas , Tbakhi Abdelghani 
Published: October 2021

AbstractSuffix trees are fundamental data structure in stringology. In this work, we introduce two algorithms that index all strings/suffixes under all internal nodes in suffix tree in linear time and space. These indexes can contribute in resolving several strings problems such as DNA sequence analysis and approximate pattern matching problems.
Involvement of mechanical cues in the migration of Cajal-Retzius cells in the marginal zone during neocortical development
Authors: López-Mengual Ana , Segura-Feliu Miriam , Sunyer Raimon , Sanz-Fraile Héctor , Otero Jorge , Mesquida-Veny Francina , Gil Vanessa , Hervera Arnau , Ferrer Isidre , Ortín Jordi , Soriano Jordi , Trepat Xavier , Farré Ramon , Navajas Daniel , del Río José A. 
Published: October 2021

AbstractEmerging evidence points to coordinated action of chemical and mechanical cues during brain development. At early stages of neocortical development, angiogenic factors and chemokines such as CXCL12, ephrins, and semaphorins assume crucial roles in orchestrating neuronal migration and axon elongation of postmitotic neurons. Here we explore the intrinsic mechanical properties of the developing marginal zone of the pallium in the migratory pathways and brain distribution of the pioneer Cajal-Retzius cells. These pioneer neurons are generated in several proliferative regions in the developing brain (e.g., the cortical hem and the pallial subpallial boundary) and migrate tangentially in the preplate/marginal zone covering the upper portion of the neocortex. These cells play crucial roles in correct neocortical layer formation by secreting several molecules such as Reelin. Our results indicate that the motogenic properties of Cajal-Retzius cells and their perinatal distribution in the marginal zone are also modulated by both chemical and mechanical factors, by the specific mechanical properties of Cajal-Retzius cells, and by the differential stiffness of the migratory routes. Indeed, cells originating in the cortical hem display higher migratory capacities than those generated in the pallial subpallial boundary which may be involved in the differential distribution of these cells in the dorsal-lateral axis in the developing marginal zone.
TGFβ signaling is required for sclerotome resegmentation during development of the spinal column in Gallus gallus
Authors: Clayton Sade W. , McCardell Ronisha , Serra Rosa 
Published: October 2021

ABSTRACTWe previously showed the importance of TGFβ signaling in development of the mouse axial skeleton. Here, we provide the first direct evidence that TGFβ signaling is required for resegmentation of the sclerotome using chick embryos. Lipophilic fluorescent tracers, DiO and DiD, were microinjected into adjacent somites of embryos treated with or without TGFβR1 inhibitor, SB431542, at developmental day E2.5 (HH16). Lineage tracing of labeled cells was observed over the course of 4 days until the completion of resegmentation at E6.5 (HH32). Vertebrae were malformed and intervertebral discs were small and misshapen in SB431542 injected embryos. Hypaxial myofibers were also increased in thickness after treatment with the inhibitor. Inhibition of TGFβ signaling resulted in alterations in resegmentation that ranged between full, partial, and slanted shifts in distribution of DiO or DiD labeled cells within vertebrae. Patterning of rostro- caudal markers within sclerotome was disrupted at E3.5 after treatment with SB431542 with rostral domains expressing both rostral and caudal markers. We propose that TGFβ signaling regulates rostro-caudal polarity and subsequent resegmentation in sclerotome during spinal column development.
The mitochondrial deubiquitinase USP30 regulates AKT/mTOR signaling
Authors: Zhang Ruohan , Ozgen Serra , Luo Hongke , Krigman Judith , Zhao Yutong , Xin Gang , Sun Nuo 
Published: October 2021

AbstractMitophagy is an intracellular mechanism to maintain mitochondrial health by removing dysfunctional mitochondria. The E3 ligase Parkin ubiquitinates the membrane proteins on targeted mitochondria to initiate mitophagy, and USP30 antagonizes this Parkin-dependent mitophagy. AKT/mTOR signaling is a master regulator of cell proliferation, differentiation, survival, and growth. Although mounting evidence showed mitophagy and AKT/mTOR signaling interact with each other during mitophagy, the specific mechanisms between Parkin/USP30 and AKT/mTOR signaling have not been elucidated. This research artificially expressed Parkin and USP30 in Hela cells and compared AKT/mTOR and apoptosis signals between Hela cells, HeLa Parkin cells, and Hela Parkin USP30 cells during mitophagy. The study’s results suggest that Parkin promotes AKT degradation via ubiquitination, which induces cell apoptosis during mitochondrial stress. On the contrary, USP30 protects AKT via deubiquitination. These findings provide new insights into Parkin and USP30’s role in cell apoptosis and physiological and pathological functions of USP30 beyond mitophagy.
KTD1 is a yeast defense factor against K28 killer toxin
Authors: Andreev Ilya , Giovanetti Simone M. , Urtecho Guillaume , Shriner Daniel , Bloom Joshua S. , Sadhu Meru J. 
Published: October 2021

AbstractSecreted protein toxins are widely used weapons in conflicts between organisms. Killer yeast produce killer toxins that inhibit the growth of nearby sensitive yeast. We investigated variation in resistance to the killer toxin K28 across diverse natural isolates of the Saccharomyces cerevisiae population and discovered a novel defense factor, which we named KTD1, that is an important determinant of K28 toxin resistance. KTD1 is a member of the DUP240 gene family of unknown function. We uncovered a putative role of DUP240 proteins in killer toxin defense and identified a region that is undergoing rapid evolution and is critical to KTD1’s protective ability. Our findings implicate KTD1 as a key factor in the defense against killer toxin K28.
A modified cut-set method for mechanical subassembly identification
Authors: Gulivindala Anil Kumar , Bahubalendruni M.V.A. Raju , Kumar Inkulu Anil , Varupala S.S. Vara Prasad , K. SankaranarayanaSamy 
Published: October 2021

Purpose
The purpose of this paper is to perform a comparative assessment on working of the existed subassembly identification (SI) methods, which are widely practiced during the product development stage and to propose an improved method for solving the SI problem in assembly sequence planning (ASP).

Design/methodology/approach
The cut-set method is found as a suitable method among various knowledge-based methods such as the theory of loops, theory of connectors and theory of clusters for the workability enhancement to meet the current requirements. Necessary product information is represented in the matrix format by replacing the traditional AND/OR graphs and the advanced predicates are included in the evaluation criteria.

Findings
The prominent methods in SI are followed a few of the predicates to avoid complexity in solution generation. The predicate consideration is found as the most influencing factor in eliminating the infeasible part combinations at SI. However, the quality of identified subassemblies without advanced predicates is not influencing the solution generation phase but practical applicability is affecting adversely.

Originality/value
The capability of performing SI by the cut-set method is improved to deal with the complex assembly configurations. The improved method is tested by applying on different assembly configurations and the effectiveness is compared with other existent methods of ASP along with the conventional method.
Didecyl dimethyl ammonium chloride as a highly efficient corrosion inhibitor for carbon steel in hydrochloric acid solution
Authors: Wei Xiaojing , Wang Jue , Shi Xin , Zhou Feng , Gao Duolong , Wen Xiaohu , Zhong Xiankang 
Published: October 2021

Purpose
This paper aims to discover a highly efficient corrosion inhibitor for 45# steel in hydrochloric acid solution and reveal the mechanism of inhibitors.

Design/methodology/approach
In this paper, electrochemical measurements, weight loss measurements, surface characterization and theoretical calculation are used to evaluate the inhibition performance and reveal the mechanism of inhibitors.

Findings
Results show that didecyl dimethyl ammonium chloride (DDAC), especially in combination with dodecane phenol plyoxyethylene, could provide a good protection performance for the carbon steel in hydrochloric acid. The N atoms and long alkyl chains in DDAC molecular structure play the vital role.

Originality/value
Usually, DDAC is used as the compound chemical disinfectant in oilfield sterilization, medicine and health. However, to the best of the authors’ knowledge, no study has shown that it can mitigate the corrosion of carbon steels in HCl solution.
Analysis and numerical solution of dynamic Jiles–Atherton model applied to hysteresis modeling for giant magnetostrictive materials
Authors: Rong Ce , He Zhongbo , Xue Guangming , Liu Guoping , Dai Bowen , Zhou Zhaoqi 
Published: October 2021

PurposeOwing to the excellent performance, giant magnetostrictive materials (GMMs) are widely used in many engineering fields. The dynamic Jiles–Atherton (J-A) model, derived from physical mechanism, is often used to describe the hysteresis characteristics of GMM. However, this model, despite cited by many different literature studies, seems not to possess unique expressions, which may cause great trouble to the subsequent application. This paper aims to provide the rational expressions of the dynamic J-A model and propose a numerical computation scheme to obtain the model results with high accuracy and fast speed.Design/methodology/approachThis paper analyzes different published papers and provides a reasonable form of the dynamic J-A model based on functional properties and physical explanations. Then, a numerical computation scheme, combining the Newton method and the explicit Adams method, is designed to solve the modified model. In addition, the error source and transmission path of the numerical solution are investigated, and the influence of model parameters on the calculation error is explored. Finally, some attempts are made to study the influence of numerical scheme parameters on the accuracy and time of the computation process. Subsequently, an optimization procedure is proposed.FindingsA rational form of the dynamic J-A model is concluded in this paper. Using the proposed numerical calculation scheme, the maximum calculation error, while computing the modified model, can remain below 2 A/m under different model parameter combinations, and the computation time is always less than 0.5 s. After optimization, the calculation speed can be enhanced with the computation accuracy guaranteed.Originality/valueTo the best of the authors’ knowledge, this paper is the first one trying to provide a rational form of the dynamic J-A model among different citations. No other research studies focus on designing a detailed computation scheme targeting the fast and accurate calculation of this model as well. And the performance of the proposed calculation method is validated in different conditions.
Effectiveness of human resource records management strategies at a university in Ghana
Authors: Adom-Nyankey Kofi , Andoh Raphael Papa Kweku 
Published: October 2021

Purpose
Human resource records are very important in the successful management of organisations. Despite their importance, they are ignored in records management studies. This study aims to bring to the limelight human resource records management issues that are overlooked despite the numerous studies on records management by examining the effectiveness of human resource records management strategies at a university in Ghana.

Design/methodology/approach
A descriptive survey was used in this study. A combination of census and simple random sampling was used to administer questionnaires to administrators who handle master or working personal files regularly. Data of 228 respondents was processed using SPSS and analysed in frequencies, percentages, mean and standard deviation.

Findings
This study revealed that while most vital documents were found on staff personal files, some documents like medical reports, passport pictures and birth certificates were somewhat unavailable. It was also found that the University had no human resource records policy in its corporate strategic thrust, which is a barrier to effective human resource records management, but the records creation strategies were effective. However, regarding the maintenance, and retention and disposition of human resource records, the strategies were ineffective. Overall, the findings fell short of the ISO 15489 framework for managing records.

Originality/value
This study seeks to bring to the fore human resource records management issues that seem to be overlooked despite the numerous studies on records management.
Evaluating methods for estimating whole house air infiltration rates in summer: implications for overheating and indoor air quality
Authors: Roberts Ben M. , Allinson David , Lomas Kevin J. 
Published: October 2021

PurposeAccurate values for infiltration rate are important to reliably estimate heat losses from buildings. Infiltration rate is rarely measured directly, and instead is usually estimated using algorithms or data from fan pressurisation tests. However, there is growing evidence that the commonly used methods for estimating infiltration rate are inaccurate in UK dwellings. Furthermore, most prior research was conducted during the winter season or relies on single measurements in each dwelling. Infiltration rates also affect the likelihood and severity of summertime overheating. The purpose of this work is to measure infiltration rates in summer, to compare this to different infiltration estimation methods, and to quantify the differences.Design/methodology/approachFifteen whole house tracer gas tests were undertaken in the same test house during spring and summer to measure the whole building infiltration rate. Eleven infiltration estimation methods were used to predict infiltration rate, and these were compared to the measured values. Most, but not all, infiltration estimation methods relied on data from fan pressurisation (blower door) tests. A further four tracer gas tests were also done with trickle vents open to allow for comment on indoor air quality, but not compared to infiltration estimation methods.FindingsThe eleven estimation methods predicted infiltration rates between 64 and 208% higher than measured. The ASHRAE Enhanced derived infiltration rate (0.41 ach) was closest to the measured value of 0.25 ach, but still significantly different. The infiltration rate predicted by the “divide-by-20” rule of thumb, which is commonly used in the UK, was second furthest from the measured value at 0.73 ach. Indoor air quality is likely to be unsatisfactory in summer when windows are closed, even if trickle vents are open.Practical implicationsThe findings have implications for those using dynamic thermal modelling to predict summertime overheating who, in the absence of a directly measured value for infiltration rate (i.e. by tracer gas), currently commonly use infiltration estimation methods such as the “divide-by-20” rule. Therefore, infiltration may be overestimated resulting in overheating risk and indoor air quality being incorrectly predicted.Originality/valueDirect measurement of air infiltration rate is rare, especially multiple tests in a single home. Past measurements have invariably focused on the winter heating season. This work is original in that the tracer gas technique used to measure infiltration rate many times in a single dwelling during the summer. This work is also original in that it quantifies both the infiltration rate and its variability, and compares these to values produced by eleven infiltration estimation methods.
Informal entrepreneurship and women's empowerment – the case of street vendors in urban Colombia
Authors: Pineda Duque Javier Armando , Castiblanco Moreno Suelen Emilia 
Published: October 2021

PurposeInternational development organizations promote access to resources through self-employment as one of the main strategies to achieve women's empowerment. However, many self-employees are more similar to informal workers than to successful entrepreneurs affecting women's control over resources and their empowerment process. This article analyzes the relationship between informal entrepreneurship and female empowerment in the context of an emerging economy.Design/methodology/approachThe authors surveyed a sample of 295 female street vendors in Bogotá – Colombia. Contingency and correlational analysis is performed.FindingsEvidence is found about the expansion of women's capacity to make decisions about resource allocation and time managing because of informal entrepreneurship. Nevertheless, these decisions are not strategic nor given in a context with several options. Several structural constraints to the exercise of agency limit empowerment to an individual process dependent on circumstances instead of a collective process resulting in changes in women's social conditions.Research limitations/implicationsThis research allows for a better understanding of the potentialities and opportunities these entrepreneurships offer to women and what strategies could be implemented to take advantage of them.Practical implicationsDespite their characteristics, informal entrepreneurship has potentialities to improve female empowerment especially when factors beyond economic rationality, such as personal, familial and sociocultural, are considered.Originality/valueThe authors discuss the category of informal entrepreneurship in emerging economies and evaluate the success of this type of entrepreneurship with a gender point of view by incorporating empowerment as measure.