bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trend in overall survival from the start of first-line chemotherapy in patients with metastatic urothelial carcinoma
Authors: Yamamoto Shoma , Kato Minoru , Matsue Taisuke , Yukimatsu Nao , Takeyama Yuji , Otoshi Taiyo , Yamasaki Takeshi , Kuratsukuri Katsuyuki , Uchida Junji 
Published: October 2023

Abstract
New approaches involving immune checkpoint inhibitors and antibody-drug conjugates prolong overall survival in patients with metastatic urothelial carcinoma. However, the access to such systemic therapy in clinical practice is suboptimal, and whether these agents improve overall survival in patients with metastatic urothelial carcinoma over time remains unclear. Hence, we investigated the overall survival trend from the initiation of first-line therapy with these agents to identify changes due to the medication and time of treatment initiation. We retrospectively evaluated 195 patients from a single center. They were treated with chemotherapy, pembrolizumab, or avelumab or enfortumab vedotin. The treatment was categorized into chemotherapy, pembrolizumab or avelumab/enfortumab vedotin period. The new agents prolonged overall survival from the start of first-line therapy. Furthermore, sequential treatment with these agents in real-world clinical practice has been reported to prolong overall survival. These study results will have major implications when a new first-line therapy is approved in the future.
The Sociopolitical History of Sun-and-Sand Tourism in Mexico: Tourist Imaginaries and Resort Development from Acapulco to Cancún
Authors: Vitz Matthew 
Published: October 2023

Abstract
Histories of Mexico’s lucrative sun-and-sand tourism development have focused overwhelmingly on economic motivations and impacts, neglecting the political dimensions of how resorts were planned and how they were experienced by working-class residents. “The Sociopolitical History of Sun-and-Sand Tourism in Mexico” argues that the spatial planning of, and mid-century political contests over, Acapulco’s tourism economy, as well as rural political discontent in Guerrero and beyond, set the political and technical parameters within which Mexican officials planned resort destinations in the 1960s and 1970s. This article builds on recent scholarship that fuses political-economic and cultural approaches to examine the political culture of resort centers, wherein the actions of both elite and popular groups explain how resort development took place in Mexico. It tells the neglected political history of resort development in Mexico, beginning with the 1940s planning of Acapulco through the populist reforms of President Luis Echeverría (1970–1976).
Modelling the AM CVn and double detonation supernova progenitor binary system CD-30°11223
Authors: Deshmukh Kunal , Bauer Evan B , Kupfer Thomas , Dorsch Matti 
Published: October 2023

ABSTRACT
We present a detailed modelling study of CD-30°11223 (CD-30), a hot subdwarf (sdB)-white dwarf (WD) binary identified as a double detonation supernova progenitor, using the open-source stellar evolution software MESA. We focus on implementing binary evolution models carefully tuned to match the observed characteristics of the system including log g and Teff. For the first time, we account for the structure of the hydrogen envelope throughout the modelling, and find that the inclusion of element diffusion is important for matching the observed radius and temperature. We investigate the two sdB mass solutions (0.47 and 0.54 M⊙) previously proposed for this system, strongly favouring the 0.47 M⊙ solution. The WD cooling age is compared against the sdB age using our models, which suggest an sdB likely older than the WD, contrary to the standard assumption for compact sdB-WD binaries. Subsequently, we propose a possible alternate formation channel for CD-30. We also perform binary evolution modelling of the system to study various aspects such as mass transfer, orbital period evolution, and luminosity evolution. Our models confirm CD-30 as a double detonation supernova progenitor, expected to explode ≈55 Myr from now. The WD accretes an ≈0.17 M⊙ thick helium shell that causes a detonation, leaving a 0.30 M⊙ sdB ejected at ≈750 km s−1. The final 15 Myr of the system are characterized by helium accretion which dominates the system luminosity, possibly resembling an AM CVn-type system.
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
Authors: Zhao Yixin , Liu Lingjie , Hassett Rebecca , Siepel Adam 
Published: October 2023

Abstract
In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions. Here, we examine the dynamics of these processes using a combination of statistical modeling, simulation, and analysis of real nascent RNA sequencing data. We develop a simple probabilistic model that jointly describes the kinetics of transcription initiation, pause-escape, and elongation, and the generation of nascent RNA sequencing read counts under steady-state conditions. We then extend this initial model to allow for variability across cells in promoter-proximal pause site locations and steric hindrance of transcription initiation from paused RNAPs. In an extensive series of simulations, we show that this model enables accurate estimation of initiation and pause-escape rates. Furthermore, we show by simulation and analysis of real data that pause-escape is often strongly rate-limiting and that steric hindrance can dramatically reduce initiation rates. Our modeling framework is applicable to a variety of inference problems, and our software for estimation and simulation is freely available.
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes
Authors: Adler Benjamin A , Trinidad Marena I , Bellieny-Rabelo Daniel , Zhang Elaine , Karp Hannah M , Skopintsev Petr , Thornton Brittney W , Weissman Rachel F , Yoon Peter H , Chen LinXing , Hessler Tomas , Eggers Amy R , Colognori David , Boger Ron , Doherty Erin E , Tsuchida Connor A , Tran Ryan V , Hofman Laura , Shi Honglue , Wasko Kevin M , Zhou Zehan , Xia Chenglong , Al-Shimary Muntathar J , Patel Jaymin R , Thomas Vienna C J X , Pattali Rithu , Kan Matthew J , Vardapetyan Anna , Yang Alana , Lahiri Arushi , Maxwell Micaela F , Murdock Andrew G , Ramit Glenn C , Henderson Hope R , Calvert Roland W , Bamert Rebecca S , Knott Gavin J , Lapinaite Audrone , Pausch Patrick , Cofsky Joshua C , Sontheimer Erik J , Wiedenheft Blake , Fineran Peter C , Brouns Stan J J , Sashital Dipali G , Thomas Brian C , Brown Christopher T , Goltsman Daniela S A , Barrangou Rodolphe , Siksnys Virginius , Banfield Jillian F , Savage David F , Doudna Jennifer A 
Published: October 2023

Abstract
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.
GenBank 2024 Update
Authors: Sayers Eric W , Cavanaugh Mark , Clark Karen , Pruitt Kim D , Sherry Stephen T , Yankie Linda , Karsch-Mizrachi Ilene 
Published: October 2023

Abstract
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 25 trillion base pairs from over 3.7 billion nucleotide sequences for 557 000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. Recent updates include policies for including spatio-temporal metadata, clarified documentation for GenBank data processing, enhanced foreign contamination screening tools, new processes in the Submission Portal, migration of Entrez Genome and Assembly displays into NCBI Datasets, and the impending retirement of tbl2asn, replaced by table2asn.
HumanLectome, an update of UniLectin for the annotation and prediction of human lectins
Authors: Schnider Boris , M’Rad Yacine , el Ahmadie Jalaa , de Brevern Alexandre G , Imberty Anne , Lisacek Frederique 
Published: October 2023

Abstract
The UniLectin portal (https://unilectin.unige.ch/) was designed in 2019 with the goal of centralising curated and predicted data on carbohydrate-binding proteins known as lectins. UniLectin is also intended as a support for the study of lectomes (full lectin set) of organisms or tissues. The present update describes the inclusion of several new modules and details the latest (https://unilectin.unige.ch/humanLectome/), covering our knowledge of the human lectome and comprising 215 unevenly characterised lectins, particularly in terms of structural information. Each HumanLectome entry is protein-centric and compiles evidence of carbohydrate recognition domain(s), specificity, 3D-structure, tissue-based expression and related genomic data. Other recent improvements regarding interoperability and accessibility are outlined.
LSM14B is essential for oocyte meiotic maturation by regulating maternal mRNA storage and clearance
Authors: Wan Yanling , Yang Shuang , Li Tongtong , Cai Yuling , Wu Xinyue , Zhang Mingyu , Muhammad Tahir , Huang Tao , Lv Yue , Chan Wai-Yee , Lu Gang , Li Jingxin , Sha Qian-Qian , Chen Zi-Jiang , Liu Hongbin 
Published: October 2023

Abstract
Fully grown oocytes remain transcriptionally quiescent, yet many maternal mRNAs are synthesized and retained in growing oocytes. We now know that maternal mRNAs are stored in a structure called the mitochondria-associated ribonucleoprotein domain (MARDO). However, the components and functions of MARDO remain elusive. Here, we found that LSM14B knockout prevents the proper storage and timely clearance of mRNAs (including Cyclin B1, Btg4 and other mRNAs that are translationally activated during meiotic maturation), specifically by disrupting MARDO assembly during oocyte growth and meiotic maturation. With decreased levels of storage and clearance, the LSM14B knockout oocytes failed to enter meiosis II, ultimately resulting in female infertility. Our results demonstrate the function of LSM14B in MARDO assembly, and couple the MARDO with mRNA clearance and oocyte meiotic maturation.
Public- and private-sector jobs: a cross-country perspective
Authors: Fenizia Alessandra , Checchi Daniele , Lucifora Claudio 
Published: October 2023

Abstract
This article reassesses the conventional wisdom that public-sector jobs have worse pay but better amenities than equivalent private-sector jobs, using data from 22 European countries and the USA. Earnings gaps are shown to be heterogeneous across countries—public sector work carries a premium in Europe but a penalty in the USA. However, whereas European public-sector workers report better job amenities—better job security and work–life balance—than their private-sector counterparts, there are no public–private amenity differentials for US workers. Public-sector work also has fewer pay-for-performance schemes. Finally, the public sector does not seem to ensure a fairer work environment, compared to the private sector, in terms of workplace discrimination and harassment. These stylized facts inform the external validity of extrapolating individual case studies to different contexts.
Clinical and Metagenomic Characterization of Neurological Infections of People With Human Immunodeficiency Virus in the Peruvian Amazon
Authors: Steinberg Hannah E , Ramachandran Prashanth S , Diestra Andrea , Pinchi Lynn , Ferradas Cusi , Kirwan Daniela E , Diaz Monica M , Sciaudone Michael , Wapniarski Annie , Zorn Kelsey C , Calderón Maritza , Cabrera Lilia , Pinedo-Cancino Viviana , Wilson Michael R , Asayag Cesar Ramal , Gilman Robert H , Bowman Natalie M ,   Toxoplasmosis Working Group in Peru, Apaza Catherine , Ayachi Melanie , Bocanegra Oliver A , Bok Jeroen , Pinedo Linda Chanamé , Urquizo Marilly Donayre , Gutierrez-Loli Renzo , Pinedo Gaston , Trompeter Grace , Vazquez Sory , Zhu Deanna 
Published: October 2023

AbstractBackgroundNeurological opportunistic infections cause significant morbidity and mortality in people with human immunodeficiency virus (HIV) but are difficult to diagnose.MethodsOne hundred forty people with HIV with acute neurological symptoms from Iquitos, Peru, were evaluated for cerebral toxoplasmosis with quantitative polymerase chain reaction (qPCR) of cerebrospinal fluid (CSF) and for cryptococcal meningitis with cryptococcal antigen test (CrAg) in serum or CSF. Differences between groups were assessed with standard statistical methods. A subset of samples was evaluated by metagenomic next-generation sequencing (mNGS) of CSF to compare standard diagnostics and identify additional diagnoses.ResultsTwenty-seven participants were diagnosed with cerebral toxoplasmosis by qPCR and 13 with cryptococcal meningitis by CrAg. Compared to participants without cerebral toxoplasmosis, abnormal Glasgow Coma Scale score (P = .05), unilateral focal motor signs (P = .01), positive Babinski reflex (P = .01), and multiple lesions on head computed tomography (CT) (P = .002) were associated with cerebral toxoplasmosis. Photophobia (P = .03) and absence of lesions on head CT (P = .02) were associated with cryptococcal meningitis. mNGS of 42 samples identified 8 cases of cerebral toxoplasmosis, 7 cases of cryptococcal meningitis, 5 possible cases of tuberculous meningitis, and incidental detections of hepatitis B virus (n = 1) and pegivirus (n = 1). mNGS had a positive percentage agreement of 71% and a negative percentage agreement of 91% with qPCR for T gondii. mNGS had a sensitivity of 78% and specificity of 100% for Cryptococcus diagnosis.ConclusionsAn infection was diagnosed by any method in only 34% of participants, demonstrating the challenges of diagnosing neurological opportunistic infections in this population and highlighting the need for broader, more sensitive diagnostic tests for central nervous system infections.
Virologic Response to Dolutegravir Plus Lamivudine in People With Suppressed Human Immunodeficiency Virus Type 1 and Historical M184V/I: A Systematic Literature Review and Meta-analysis
Authors: Kabra Madhusudan , Barber Tristan J , Allavena Clotilde , Marcelin Anne-Geneviève , Di Giambenedetto Simona , Pasquau Juan , Gianotti Nicola , Llibre Josep M , Rial-Crestelo David , De Miguel-Buckley Rosa , Blick Gary , Turner Matthew , Harrison Cale , Wynne Tammy , Verdier Gustavo , Parry Chris M , Jones Bryn , Okoli Chinyere , Donovan Cynthia , Priest Julie , Letang Emilio 
Published: October 2023

Abstract

Background
To investigate the impact of the M184V/I mutation on virologic response to dolutegravir plus lamivudine (DTG + 3TC) in suppressed-switch populations, a meta-analysis was performed using virologic outcomes from people with human immunodeficiency virus type 1 (PWH) with and without M184V/I before DTG + 3TC switch in real-world studies identified via systematic literature review. Sensitivity analyses were performed using data from PWH with M184V/I in interventional studies identified via targeted literature review.

Methods
Single-arm meta-analyses using common- and random-effects models were used to estimate proportions of PWH with virologic failure (VF) among real-world populations with and without M184V/I and interventional study participants with M184V/I at 24, 48, and 96 weeks.

Results
Literature reviews identified 5 real-world studies from 3907 publications and 51 abstracts meeting inclusion criteria and 5 interventional studies from 1789 publications and 3 abstracts. All time points had low VF incidence in PWH with M184V/I (real-world: 1.43%–3.81%; interventional: 0.00%) and without (real-world: 0.73%–2.37%). Meta-analysis–estimated proportions (95% confidence interval) with VF were low at weeks 24, 48, and 96, respectively, for PWH with M184V/I (real-world: 0.01 [.00–.04], 0.03 [.01–.06], and 0.04 [.01–.07]; interventional: 0.00 [.00–.02], 0.00 [.00–.01], and 0.00 [.00–.03]) and without (real-world: 0.00 [.00–.02], 0.02 [.01–.04], and 0.02 [.00–.05]). One real-world study (n = 712) reported treatment-emergent M184V at VF in 1 of 652 (0.15%) PWH without prior M184V/I.

Conclusions
Results suggest that prior M184V/I has minimal impact on virologic suppression after switching to DTG + 3TC and provide reassurance when considering switching regimens in virologically suppressed PWH with incomplete treatment history or limited treatment options.
Seimei/KOOLS-IFU mapping of the gas and dust distributions in Galactic PNe: Unveiling the origin and evolution of the Galactic halo PN H4-1
Authors: Otsuka Masaaki , Ueta Toshiya , Tajitsu Akito 
Published: October 2023

Abstract
H4-1 is a planetary nebula (PN) located in the Galactic halo, and is notably carbon-rich and one of the most metal-deficient PNe in the Milky Way. To unveil its progenitor evolution through accurate measurement of the gas mass, we conducted a comprehensive investigation of H4-1, using the newly obtained Seimei/KOOLS-IFU spectra and multiwavelength spectro-photometry data. The emission-line images generated from the KOOLS-IFU data cube successfully resolve the ellipsoidal nebula and the equatorial flattened disk that are frequently seen in bipolar PNe evolved from massive progenitors. By a fully data-driven method, we directly derived the seven elemental abundances, the gas-to-dust mass ratio, and the gas and dust masses based on our own distance scale. By comparing the observed quantities with both the photoionization model and the binary nucleosynthesis model, we conclude that the progenitors of initial masses of 1.87 M$_{\odot }$ and 0.82 M$_{\odot }$ are second-generation stars formed ∼4 Gyr after the Big Bang that have undergone mass transfers and a binary merger, and have ultimately evolved into a PN showing unique chemical abundances. Our binary model successfully reproduces the observed abundances and also explains the evolutionary time scale of H4-1.
Neighboring inteins interfere with one another's homing capacity
Authors: Turgeman-Grott Israela , Arsenault Danielle , Yahav Dekel , Feng Yutian , Miezner Guy , Naki Doron , Peri Omri , Papke R Thane , Gogarten Johann Peter , Gophna Uri 
Published: October 2023

Abstract
Inteins are mobile genetic elements that invade conserved genes across all domains of life and viruses. In some instances, a single gene will have several intein insertion sites. In Haloarchaea, the minichromosome maintenance (MCM) protein at the core of replicative DNA helicase contains four intein insertion sites within close proximity, where two of these sites (MCM-a and MCM-d) are more likely to be invaded. A haloarchaeon that harbors both MCM-a and MCM-d inteins, Haloferax mediterranei, was studied in vivo to determine intein invasion dynamics and the interactions between neighboring inteins. Additionally, invasion frequencies and the conservation of insertion site sequences in 129 Haloferacales mcm homologs were analyzed to assess intein distribution across the order. We show that the inteins at MCM-a and MCM-d recognize and cleave their respective target sites and, in the event that only one empty intein invasion site is present, readily initiate homing (i.e. single homing). However, when two inteins are present co-homing into an intein-free target sequence is much less effective. The two inteins are more effective when invading alleles that already contain an intein at one of the two sites. Our in vivo and computational studies also support that having a proline in place of a serine as the first C-terminal extein residue of the MCM-d insertion site prevents successful intein splicing, but does not stop recognition of the insertion site by the intein's homing endonuclease.
Comprehensive assessment of sleep duration, insomnia, and brain structure within the UK Biobank cohort
Authors: Stolicyn Aleks , Lyall Laura M , Lyall Donald M , Høier Nikolaj Kjær , Adams Mark J , Shen Xueyi , Cole James H , McIntosh Andrew M , Whalley Heather C , Smith Daniel J 
Published: October 2023

AbstractStudy ObjectivesTo assess for associations between sleeping more than or less than recommended by the National Sleep Foundation (NSF), and self-reported insomnia, with brain structure.MethodsData from the UK Biobank cohort were analyzed (N between 9K and 32K, dependent on availability, aged 44 to 82 years). Sleep measures included self-reported adherence to NSF guidelines on sleep duration (sleeping between 7 and 9 hours per night), and self-reported difficulty falling or staying asleep (insomnia). Brain structural measures included global and regional cortical or subcortical morphometry (thickness, surface area, volume), global and tract-related white matter microstructure, brain age gap (difference between chronological age and age estimated from brain scan), and total volume of white matter lesions.ResultsLonger-than-recommended sleep duration was associated with lower overall grey and white matter volumes, lower global and regional cortical thickness and volume measures, higher brain age gap, higher volume of white matter lesions, higher mean diffusivity globally and in thalamic and association fibers, and lower volume of the hippocampus. Shorter-than-recommended sleep duration was related to higher global and cerebellar white matter volumes, lower global and regional cortical surface areas, and lower fractional anisotropy in projection fibers. Self-reported insomnia was associated with higher global gray and white matter volumes, and with higher volumes of the amygdala, hippocampus, and putamen.ConclusionsSleeping longer than recommended by the NSF is associated with a wide range of differences in brain structure, potentially indicative of poorer brain health. Sleeping less than recommended is distinctly associated with lower cortical surface areas. Future studies should assess the potential mechanisms of these differences and investigate long sleep duration as a putative marker of brain health.