bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Mutations via Chern–Simons Currents
Authors: Bajardi Francesco , Altucci Lucia , Benedetti Rosaria , Capozziello Salvatore , Sorbo Maria Rosaria Del , Franci Gianluigi , Altucci Carlo 
Published: October 2021

AbstractWe test the validity of a possible schematization of DNA structure and dynamics based on the Chern–Simons theory, that is a topological field theory mostly considered in the context of effective gravity theories. By means of the expectation value of the Wilson Loop, derived from this analogue gravity approach, we find the point-like curvature of genomic strings in KRAS human gene and COVID-19 sequences, correlating this curvature with the genetic mutations. The point-like curvature profile, obtained by means of the Chern–Simons currents, can be used to infer the position of the given mutations within the genetic string. Generally, mutations take place in the highest Chern–Simons current gradient locations and subsequent mutated sequences appear to have a smoother curvature than the initial ones, in agreement with a free energy minimization argument.
On the module of derivations of rings of invariants of k[X,Y ] under the action of certain dihedral groups
Authors: Dey Arindam , Kour Surjeet 
Published: October 2021

In this paper, we study the derivation module of the ring of invariants of [Formula: see text] under the linear action of dihedral groups [Formula: see text] mentioned in a paper by Riemenschneider [Die Invarianten der endlichen Untergruppen von [Formula: see text], Math. Zeitsch. 153 (1977) 37–50]. We obtained an explicit generating set for the derivation module of [Formula: see text]. We show that [Formula: see text].
Role of Physicochemical Factors on the Efficacy and Safety of Lipid-Based Nanosystems as Potential Drug Carriers
Authors: Aghajani Mahdi , Arbabi Bidgoli Sepideh , Tavakol Kamran 
Published: October 2021

The efficacy and safety are two challenging factors before trusting the lipid-based Nanosystems (LBNs) for diagnostic and therapeutic purposes. The aim of this paper is to evaluate the accessible in-vitro and in-vivo studies on the contribution of major physicochemical factors of LBNs for the effective and safe delivery of drugs and anticancer agents into the target site. These factors included lipid charge, particle size and size distribution, lipid composition and components, surface hydrophilicity and hydrophobicity, and surface coating. Here, reliable databases were searched for full-text, accessible and original articles to conduct this review. We included relevant studies since 1992, which were conducted on the development of LBNs for therapeutic and diagnostic purposes. Many studies have shown that using polyethylene glycol modification reduces the undesirable side effects and controls the efficacy and toxicity for in-vitro and in-vivo delivery of drugs or anticancer agents. Also, optimization of the size and composition of lipid nanoparticles minimizes the toxicity of the anticancer agents associated with a carrier. In addition, the presence of positively charged lipids in LBNs improves the efficacy of encapsulated drugs in spite of low blood circulation efficiency and high toxicity effects. The identification of important factors involved in the delivery of LBNs as potential drug carriers is crucial and contributes to the proper design of these interesting carriers for both therapeutic and diagnostic purposes.
A Quest for the Origin of the Uneven Spread of Covid-19 Cases
Authors: Bhadra Arunava , Bhattacharya Mahasweta 
Published: October 2021

For more than one and a half years now, the world is highly impacted by the Covid-19 pandemic. The Covid-19 cases are, however, not evenly distributed across the countries; a few countries, particularly high-income countries have been hit harder than the countries of weak economic condition. The reasons for such an asymmetrical distribution are not clearly understood yet. In this work, we have examined the unevenness of global distribution of Covid-19 incidences till 18th June 2021 in terms of the economic condition of countries. Subsequently, we have tried to identify the main underlying factors behind unequal Covid-19 cases. Our analysis suggests that the physical connectivity and the diffusion of coronavirus are the main causes of the different unequal spread of Covid-19 cases in different countries. We find that the Covid-19 infected and death cases are well described by a power law in terms of the stated parameters.
Shadow Program Committee Initiative
Authors: Thongtanunam Patanamon , Rastogi Ayushi , Khomh Foutse , Demeyer Serge , Nagappan Meiyappan , Blincoe Kelly , Robles Gregorio 
Published: October 2021

The Shadow Program Committee (PC) is an initiative/program that provides an opportunity to Early-Career Researchers (ECRs), i.e., PhD students, postdocs, new faculty members, and industry practitioners, who have not been in a PC, to learn rst-hand about the peer-review process of the technical track at Software Engi- neering (SE) conferences. This program aims to train the next generation of PC members as well as to allow ECRs to be recog- nized and embedded in the research community. By participating in this program, ECRs will have a great chance i) to gain expe- rience about the reviewing process including the restrictions and ethical standards of the academic peer-review process; ii) to be mentored by senior researchers on how to write a good review; and iii) to create a network with other ECRs and senior researchers (i.e., Shadow PC advisors).
The Shadow PC program was rst introduced to the SE research community at the Mining Software Repositories (MSR) confer- ence in 2021. The program was led by Patanamon Thongta- nunam and Ayushi Rastogi (Shadow PC Co-chairs) with support from Shadow PC Advisor Co-Chairs (Foutse Khomh and Serge Demeyer), PC Co-Chairs of the technical track (Meiyappan Na- gappan and Kelly Blincoe), and the General Chair of the con- ference, Gregorio Robles. To promote and facilitate the Shadow PC program at SE conferences in the future, this report provides details about the process and a re ection on the Shadow PC pro- gram during MSR2021. The presentation slides and video are also available online at https://youtu.be/ReUXwmtIEk8.
Genetic Improvement @ ICSE 2021
Authors: Brownlee Alexander E. I. 
Published: October 2021

Following Dr. Stephanie Forrest of Arizona State University's keynote presentation there was a wide ranging discussion at the tenth international Genetic Improvement workshop, GI-2021 @ ICSE (held as part of the International Conference on Software Engineering on Sunday 30th May 2021). Topics included a growing range of target systems and appli- cations, algorithmic improvements, wide-ranging questions about how other elds (especially evolutionary computation) can inform advances in GI, and about how GI is 'branded' to other disciplines.
We give a personal perspective on the workshop's proceedings, the discussions that took place, and resulting prospective directions for future research.
Transcriptional Reprogramming Differentiates Active from Inactive ESR1 Fusions in Endocrine Therapy-Refractory Metastatic Breast Cancer
Authors: Gou Xuxu , Anurag Meenakshi , Lei Jonathan T. , Kim Beom-Jun , Singh Purba , Seker Sinem , Fandino Diana , Han Airi , Rehman Saif , Hu Jianhong , Korchina Viktoriya , Doddapaneni Harshavardhan , Dobrolecki Lacey E. , Mitsiades Nicholas , Lewis Michael T. , Welm Alana L. , Li Shunqiang , Lee Adrian V. , Robinson Dan R. , Foulds Charles E. , Ellis Matthew J. 
Published: October 2021

AbstractGenomic analysis has recently identified multiple ESR1 gene translocations in estrogen receptor alpha–positive (ERα+) metastatic breast cancer (MBC) that encode chimeric proteins whereby the ESR1 ligand binding domain (LBD) is replaced by C-terminal sequences from many different gene partners. Here we functionally screened 15 ESR1 fusions and identified 10 that promoted estradiol-independent cell growth, motility, invasion, epithelial-to-mesenchymal transition, and resistance to fulvestrant. RNA sequencing identified a gene expression pattern specific to functionally active ESR1 gene fusions that was subsequently reduced to a diagnostic 24-gene signature. This signature was further examined in 20 ERα+ patient-derived xenografts and in 55 ERα+ MBC samples. The 24-gene signature successfully identified cases harboring ESR1 gene fusions and also accurately diagnosed the presence of activating ESR1 LBD point mutations. Therefore, the 24-gene signature represents an efficient approach to screening samples for the presence of diverse somatic ESR1 mutations and translocations that drive endocrine treatment failure in MBC.Significance:This study identifies a gene signature diagnostic for functional ESR1 fusions that drive poor outcome in advanced breast cancer, which could also help guide precision medicine approaches in patients harboring ESR1 mutations.
Taming the Wild-Type Gastrointestinal Stromal Tumor: Improved Tissue Culture
Authors: Blakely Andrew M. , Glod John W. , Wedekind Malone Mary Frances 
Published: October 2021

Abstract
Wild-type gastrointestinal stromal tumors (WT GIST) are most frequently characterized by succinate dehydrogenase (SDH) deficiency. Reliable ex vivo tumor models have been difficult to develop given the downstream metabolic effects of SDH deficiency. Improved tumor modeling approaches are needed to develop effective systemic treatment options for patients with WT GIST.
See related article by Yebra et al., p. 187
Birds of the Pantanal floodplains, Brazil: historical data, diversity, and conservation
Authors: Nunes Alessandro Pacheco , Posso Sérgio Roberto , Frota Angélica Vilas Boas da , Vitorino Breno Dias , Laps Rudi Ricardo , Donatelli Reginaldo José , Straube Fernando Costa , Pivatto Maria Antonietta Castro , Oliveira Dalci Maurício Miranda de , Carlos Braulio , Melo Alyson Vieira de , Tomas Walfrido Moraes , Freitas Gabriel Oliveira de , Souza Rafael Augusto Ducel de , Benites Maristela , Mamede Simone , Moreira Renato Soares 
Published: October 2021

The Pantanal floodplains of Brazil are a region of rich biodiversity. To date, the true richness of the Pantanal avifauna has not been explored satisfactorily caused by a lack of studies in the region and, especially, by the divergence of opinion among the works published by various authors on the many species found in the region. This is due to the lack of criteria in examining records, both with regard to the reliability of the identifications and in the precise geographical allocation. Therefore, in the study, we collage findings from various studies and records created by us in the last few decades from 199 distinct locations to produce a list of birds in the Pantanal floodplains. We grouped the results into three lists: primary, secondary, and tertiary. We found that the avifauna of the Pantanal floodplain is composed of a total of 617 species, of which 571 (92%) have supporting records of occurrence (primary list) and 46 still lack documentation (secondary list). The number of species listed here for the Pantanal floodplain represents 32% of all avifauna known to the Brazilian territory. This reflects the importance of the biome, as part of the national territory, for the maintenance of a meaningful avifaunistic richness. Migratory birds (n = 183), notably northern ones (n = 43), are among the main players involved in ecological processes of nutrient cycling and dispersion of important pathogens between the two continents. With regard to conservation, 25 species are included in some category of threat in the lists of threatened species with global extinction. We hope that our list will help future researchers a more definitive approach when researching the avian fauna in this bountiful region.
Revisiting the morphology of the Cretaceous ommatid beetle Clessidromma palmeri (Coleoptera: Archostemata: Ommatidae)
Authors: Li Yan-Da , Cai Chen-Yang 
Published: October 2021

The morphology of Clessidromma palmeri Jarzembowski et al. from mid-Cretaceous Burmese amber is revised based on a reexamination of the type specimen. Contrary to previous studies, our observation confirms that Clessidromma has open procoxal cavities. The characters such as platform on the ventral side of head, modified metacoxae, and ridges on head and pronotum are suggested to be diagnostic characters for Clessidromma. Clessidromma zengi Kirejtshuk from the same deposit is transferred into a new genus, as Kirejtomma zengi comb. nov.
Identification of Endothelial Proteins in Plasma Associated With Cardiovascular Risk Factors
Authors: Iglesias Maria J. , Kruse Larissa D. , Sanchez-Rivera Laura , Enge Linnea , Dusart Philip , Hong Mun-Gwan , Uhlén Mathias , Renné Thomas , Schwenk Jochen M. , Bergstrom Göran , Odeberg Jacob , Butler Lynn M. 
Published: October 2021

Objective:
Endothelial cell (EC) dysfunction is a well-established response to cardiovascular disease risk factors, such as smoking and obesity. Risk factor exposure can modify EC signaling and behavior, leading to arterial and venous disease development. Here, we aimed to identify biomarker panels for the assessment of EC dysfunction, which could be useful for risk stratification or to monitor treatment response.

Approach and Results:
We used affinity proteomics to identify EC proteins circulating in plasma that were associated with cardiovascular disease risk factor exposure. Two hundred sixteen proteins, which we previously predicted to be EC-enriched across vascular beds, were measured in plasma samples (N=1005) from the population-based SCAPIS (Swedish Cardiopulmonary Bioimage Study) pilot. Thirty-eight of these proteins were associated with body mass index, total cholesterol, low-density lipoprotein, smoking, hypertension, or diabetes. Sex-specific analysis revealed that associations predominantly observed in female- or male-only samples were most frequently with the risk factors body mass index, or total cholesterol and smoking, respectively. We show a relationship between individual cardiovascular disease risk, calculated with the Framingham risk score, and the corresponding biomarker profiles.

Conclusions:
EC proteins in plasma could reflect vascular health status.
Soluble Urokinase Plasminogen Activator Receptor: Genetic Variation and Cardiovascular Disease Risk in Black Adults
Authors: Olson Nels C. , Raffield Laura M. , Moxley Anne H. , Miller-Fleming Tyne W. , Auer Paul L. , Franceschini Nora , Ngo Debby , Thornton Timothy A. , Lange Ethan M. , Li Yun , Nickerson Deborah A. , Zakai Neil A. , Gerszten Robert E. , Cox Nancy J. , Correa Adolfo , Mohlke Karen L. , Reiner Alexander P. 
Published: October 2021

Background:
suPAR (Soluble urokinase plasminogen activator receptor) has emerged as an important biomarker of coagulation, inflammation, and cardiovascular disease (CVD) risk. The contribution of suPAR to CVD risk and its genetic influence in Black populations have not been evaluated.

Methods:
We measured suPAR in 3492 Black adults from the prospective, community-based JHS (Jackson Heart Study). Cross-sectional associations of suPAR with lifestyle and CVD risk factors were assessed, whole-genome sequence data were used to evaluate genetic associations of suPAR, and relationships of suPAR with incident CVD outcomes and overall mortality were estimated over follow-up.

Results:

In Cox models adjusted for traditional CVD risk factors, estimated glomerular filtration rate, and CRP (C-reactive protein), each 1-SD higher suPAR was associated with a 21% to 31% increased risk of incident coronary heart disease, heart failure, stroke, and mortality. In the genome-wide association study, 2 missense (rs399145 encoding p.Thr86Ala, rs4760 encoding p.Phe272Leu) and 2 noncoding regulatory variants (rs73935023 within an enhancer element and rs4251805 within the promoter) of
PLAUR
on chromosome 19 were each independently associated with suPAR and together explained 14% of suPAR phenotypic variation. The allele frequencies of each of the four suPAR-associated genetic variants differ considerably across African and European populations. We further show that
PLAUR
rs73935023 can alter transcriptional activity in vitro. We did not find any association between genetically determined suPAR and CVD in JHS or a larger electronic medical record-based analyses of Blacks or Whites.

Conclusions:
Our results demonstrate the importance of ancestry-differentiated genetic variation on suPAR levels and indicate suPAR is a CVD biomarker in Black adults.
Long-Term Impact of Urgent Secondary Prevention After Transient Ischemic Attack and Minor Stroke: Ten-Year Follow-Up of the EXPRESS Study
Authors: Luengo-Fernandez Ramon , Li Linxin , Silver Louise , Gutnikov Sergei , Beddows Nicola C. , Rothwell Peter M. 
Published: October 2021

Background and Purpose:
Urgent assessment aimed at reducing stroke risk after transient ischemic attack or minor stroke is cost-effective over the short-term. However, it is unclear if the short-term impact is lost on long-term follow-up, with recurrent events being delayed rather than prevented. By 10-year follow-up of the EXPRESS study (Early Use of Existing Preventive Strategies for Stroke), previously showing urgent assessment reduced 90-day stroke risk by 80%, we determined whether that early benefit was still evident long-term for stroke risk, disability, and costs.

Methods:
EXPRESS was a prospective population-based before (phase 1: April 2002–September 2004; n=310) versus after (phase 2: October 2004–March 2007; n=281) study of the effect of early assessment and treatment of transient ischemic attack/minor stroke on early recurrent stroke risk, with an external control. This report assesses the effect on 10-year recurrent stroke risk, functional outcomes, quality-of-life, and costs.

Results:

A reduction in stroke risk in phase 2 was still evident at 10 years (55/23.3% versus 82/31.6%; hazard ratio=0.68 [95% CI, 0.48–0.95];
P
=0.024), as was the impact on risk of disabling or fatal stroke (17/7.7% versus 32/13.1%; hazard ratio=0.54 [0.30–0.97];
P
=0.036). These effects were due to maintenance of the early reduction in stroke risk, with neither additional benefit nor rebound catch-up after 90 days (post-90 days hazard ratio=0.88 [0.65–1.44],
P
=0.88; and hazard ratio=0.83 [0.42–1.65],
P
=0.59, respectively). Disability-free life expectancy was 0.59 (0.03–1.15;
P
=0.043) years higher in patients in phase 2, as was quality-adjusted life expectancy (0.49 [0.03–0.95];
P
=0.036). Overall, 10-year costs were nonsignificantly higher in patients attending the phase 2 clinic ($1022 [-3865–5907];
P
=0.66). The additional cost per quality-adjusted life year gained in phase 2 versus phase 1 was $2103, well below current cost-effectiveness thresholds.

Conclusions:
Urgent assessment and treatment of patients with transient ischemic attack or minor stroke resulted in a long-term reduction in recurrent strokes and improved outcomes, with little atrophy of the early benefit over time, representing good value for money even with a 10-year time horizon. Our results suggest that other effective acute treatments in transient ischemic attack/minor stroke in the short-term will also have the potential to have long-term benefit.
Burster Reconstruction Considering Unmeasurable Variables in the Epileptor Model
Authors: Brogin João Angelo Ferres , Faber Jean , Bueno Douglas Domingues 
Published: October 2021

Abstract
Epilepsy is one of the most common brain disorders worldwide, affecting millions of people every year. Although significant effort has been put into better understanding it and mitigating its effects, the conventional treatments are not fully effective. Advances in computational neuroscience, using mathematical dynamic models that represent brain activities at different scales, have enabled addressing epilepsy from a more theoretical standpoint. In particular, the recently proposed Epileptor model stands out among these models, because it represents well the main features of seizures, and the results from its simulations have been consistent with experimental observations. In addition, there has been an increasing interest in designing control techniques for Epileptor that might lead to possible realistic feedback controllers in the future. However, such approaches rely on knowing all of the states of the model, which is not the case in practice. The work explored in this letter aims to develop a state observer to estimate Epileptor's unmeasurable variables, as well as reconstruct the respective so-called bursters. Furthermore, an alternative modeling is presented for enhancing the convergence speed of an observer. The results show that the proposed approach is efficient under two main conditions: when the brain is undergoing a seizure and when a transition from the healthy to the epileptiform activity occurs.
Electrospun regenerated silk fibroin is a promising biomaterial for the maintenance of inner ear progenitors in vitro
Authors: Li Guangfei , Yin Yanbo , Zhang Yaopeng , Wu Jingfang , Sun Shan 
Published: October 2021

Objective We sought to determine the biocompatibility of electrospun regenerated silk fibroin (RSF) mats with inner ear progenitors, especially their effect on the differentiation of inner ear progenitors into hair cells. Methods Neonatal mouse cochleae (n = 20) were collected and digested and allowed to form spheres over several days. Cells digested from the spheres were then seeded onto aligned or random RSF mats, with laminin-coated coverslips serving as controls. The inner ear progenitor cell mortality was examined by TUNEL labeling, and the adhesion of cells to the RSF mats or coverslip was determined by scanning electron microscopy. Finally, the number of hair cells that differentiated from inner ear progenitors was determined by Myosin7a expression. Unpaired Student’s t-tests and one-way ANOVA followed by a Dunnett’s multiple comparisons test were used in this study ( p < 0.05). Results After 5 days of culture, the inner ear progenitors had good adhesion to both the aligned and random RSF mats and there was no significant difference in TUNEL+ cells between the mats compared to the coverslip ( p > 0.05). After 7 days of in vitro differentiation culture, the percentage of differentiated hair cells on the control, aligned, and random RSF mats was 2.5 ± 0.5%, 2.7 ± 0.4%, and 2.4 ± 0.2%, respectively, and there was no significant difference between Myosin7a+ cells on either RSF mat compared to controls ( p > 0.05). Conclusion The aligned and random RSF mats had excellent biocompatibility with inner ear progenitors and helped the inner ear progenitors maintain their stemness. Our results thus indicate that RSF mats represent a useful scaffold for the development of new strategies for inner ear tissue engineering research.