bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of trastuzumab emtansine (T-DM1) on spleen volume in patients with HER2-positive metastatic breast cancer
Authors: Akyildiz Arif , Ismayilov Rashad , Abdurrahimli Najmaddin , Ormanci Aylin , Guven Deniz Can , Tuncel Murat , Onur Mehmet Ruhi , Aksoy Sercan 
Published: October 2024

Abstract

Background
Trastuzumab emtansine (T-DM1) is a novel therapy for human epidermal growth factor receptor 2 (HER2)-positive metastatic breast cancer, combining the targeted action of trastuzumab with the cytotoxic effects of emtansine. Although T-DM1 has demonstrated greater efficacy and safety compared to traditional therapies, concerns about hepatotoxicity and spleen-related complications have arisen.

Methods
We conducted a retrospective study of 64 HER2-positive metastatic breast cancer patients treated with T-DM1 at our institution. Patients underwent computed tomography or magnetic resonance imaging at baseline and during treatment cycles. Spleen volume, portal vein diameter, and laboratory values were compared between baseline and 12 months after T-DM1 treatment.

Results
Median spleen volume significantly increased from 201 cm3 (IQR, 157–275) at baseline to 291 cm3 (IQR, 215–420) after 12 months of T-DM1 treatment (P &lt; 0.001). Spleen enlargement was observed in 87.5% of patients, while no significant alteration was detected in portal vein diameter. The change in spleen volume was positively correlated with changes in serum globulin levels, liver enzymes, and bilirubin levels, but did not impact survival outcomes.

Conclusions
T-DM1 therapy in HER2-positive metastatic breast cancer leads to significant spleen enlargement and systemic biochemical changes. Future studies should focus on elucidating the long-term implications of these findings and optimizing monitoring strategies for spleen-related complications.
Gender differences in the health workforce in China: an analysis of national data
Authors: Yu Wenya , Liu Xiang , Chen Hong , Tian Jiahe , Li Meina , Mu Wei , Ge Yang 
Published: October 2024

Abstract
Gender differences in the health workforce matter for women's health and healthcare, and is also crucial for both health and economic development. Drawing on limited national gender data from China over the last 10 years, during which the country was undergoing a healthcare reform, this study dissects gender-related issues to identify existing problems, monitor progress, and develop strategies to promote change. Although women constituted the majority of health workers, they are predominantly engaged in service-oriented occupations. The gender distribution substantially differed between urban and rural primary health institutions. Moreover, significant differences in gender distribution among professional public health institutions were observed. The gender distribution of administrators varied in different types of health institutions. Women had lighter workloads because of the imbalanced distribution of specialties. Academicians comprised very few female scientists. To promote a more balanced gender distribution, policies should be developed to encourage a more reasonable division of family responsibilities. Further, equal higher education opportunities should be ensured for girls, especially in rural areas. Solutions to free more women from work–marriage–childcare conflicts and to decrease turnover rates deserve further discussion. Gender data should be highlighted and optimized to further advance gender differences among the health workforce and for women's health in China.
Importance of high suspicion of intestinal perforation in blunt abdominal injury in patients with inflammatory bowel disease
Authors: El-Diaz Nadia , Goutham Meera , Sheth Hemant 
Published: October 2024

Abstract
Estimated to affect 3 million individuals in Europe alone, Crohn’s disease is an inflammatory bowel disease causing transmural inflammation throughout the gastrointestinal tract. We describe the case of a patient with a known background of Crohn’s disease who presented with abdominal pain following blunt abdominal trauma after a hit and run where initial diagnosis of perforation was missed on pan-computed tomography, however, diagnosis was made early due to high clinical suspicion of perforation. This suggests that current diagnostic imaging can be inaccurate, leading to delays where urgent surgery is otherwise indicated which is a cause for concern. Herein, we emphasize the importance of a high index of suspicion for perforation in patients with blunt abdominal trauma, especially where there is underlying bowel disease.
Coherence via focusing for symmetric skew monoidal and symmetric skew closed categories
Authors: Veltri Niccolò 
Published: October 2024

Abstract
The symmetric skew monoidal categories of Bourke and Lack are a weakening of Mac Lane’s symmetric monoidal categories where (i) the three structural laws of left and right unitality and associativity are not required to be invertible, they are merely natural transformations with a specific orientation; (ii) the structural law of symmetry is a natural isomorphism involving three objects rather than two. In a similar fashion, symmetric skew closed categories are a weakening of de Schipper’s symmetric closed categories with non-invertible structural laws of left and right unitality. In this paper, we study the structural proof theory of symmetric skew monoidal and symmetric skew closed categories, progressing the project initiated by Uustalu et al. on deductive systems for categories with skew structure. We discuss three equivalent presentations of the free symmetric skew monoidal (resp. closed) category on a set of generating objects: a Hilbert-style categorical calculus; a cut-free sequent calculus; a focused subsystem of derivations, corresponding to a sound and complete goal-directed proof search strategy for the cut-free sequent calculus. Focusing defines an effective normalization procedure for maps in the free symmetric skew monoidal (resp. closed) category, as such solving the coherence problem for symmetric skew monoidal (resp. closed) categories.
Evolution of the dual AGN in Mrk 266: a young AGN and a rotation-dominated disc in the SW nucleus
Authors: Ruby Mason , Müller-Sánchez Francisco , Comerford Julia M , Stern Daniel , Cales Sabrina L , Harrison Fiona , Malkan Matthew A , Privon George C , Treister Ezequiel 
Published: October 2024

ABSTRACT
Dual active galactic nuclei (AGNs) offer a unique opportunity to probe the relationship between supermassive black holes (SMBH) and their host galaxies as well as the role of major mergers in triggering AGN activity. The confirmed dual AGN Mrk 266 has been studied extensively with multiwavelength imaging. Now, high-spatial-resolution IFU spectroscopy of Mrk 266 provides an opportunity to probe the kinematics of both the merger event and AGN feedback. We present for the first time high-spatial-resolution kinematic maps for both nuclei of Mrk 266 obtained with the Keck OSIRIS IFU spectrograph, utilizing adaptive optics to achieve a resolution of $0.31$ and $0.20\,\mathrm{ arcsec}$ for the NE and SW nuclei, respectively. Using the $M_\text{BH} \!-\! \sigma _*$ relation for mergers, we infer an SMBH mass of approximately $7 \times 10^{7}\, \mathrm{M}_{\odot }$ for the south-western nucleus. Additionally, we report that the molecular gas kinematics of the south-western nucleus are dominated by rotation rather than large-scale chaotic motions. The south-west nucleus also contains both a circumnuclear ring of star formation from which an inflow of molecular gas is likely fuelling the AGN and a compact, AGN-dominated outflow of highly ionized gas with a time-scale of approximately 2 Myr, significantly shorter than the time-scale of the merger. The north-eastern nucleus, on the other hand, exhibits complex kinematics related to the merger, including molecular gas that appears to have decoupled from the rotation of the stars. Our results suggest that while the AGN activity in Mrk 266 was likely triggered during the merger, AGN feeding is currently the result of processes internal to each host galaxy, thus resulting in a strong asymmetry between the two nuclei.
Atmospheric escape in hot Jupiters under sub-Alfvénic interactions
Authors: Presa Andrés , Driessen Florian A , Vidotto Aline A 
Published: October 2024

ABSTRACT
Hot Jupiters might reside inside the Alfvén surface of their host star wind, where the stellar wind is dominated by magnetic energy. The implications of such a sub-Alfvénic environment for atmospheric escape are not fully understood. Here, we employ 3D radiation-magnetohydrodynamic simulations and Ly-$\alpha$ transit calculations to investigate atmospheric escape properties of magnetized hot Jupiters. By varying the planetary magnetic field strength ($B_\mathrm{p}$) and obliquity, we find that the structure of the outflowing atmosphere transitions from a magnetically unconfined regime, where a tail of material streams from the nightside of the planet, to a magnetically confined regime, where material escapes through the polar regions. Notably, we find an increase in the planet escape rate with $B_\mathrm{p}$ in both regimes, with a local decrease when the planet transitions from the unconfined to the confined regime. Contrary to super-Alfvénic interactions, which predicted two polar outflows from the planet, our sub-Alfvénic models show only one significant polar outflow. In the opposing pole, the planetary field lines connect to the star. Finally, our synthetic Ly-$\alpha$ transits show that both the red-wing and blue-wing absorptions increase with $B_\mathrm{p}$. Furthermore, there is a degeneracy between $B_\mathrm{p}$ and the stellar wind mass-loss rate when considering absorption of individual Ly-$\alpha$ wings. This degeneracy can be broken by considering the ratio between the blue-wing and the red-wing absorptions, as stronger stellar winds result in higher blue-to-red absorption ratios. We show that, by using the absorption ratios, Ly-$\alpha$ transits can probe stellar wind properties and exoplanetary magnetic fields.
3D hydrodynamic simulations of white dwarf–main-sequence star collisions – I. Head-on collisions
Authors: van der Merwe C J T , Mohamed S S , José J , Shara M , Kamiński T 
Published: October 2024

ABSTRACT
Recently inaugurated telescopes, such as the MeerKAT radio telescope and the upcoming Rubin Observatory Legacy Survey of Space and Time, will be able to detect millions of transient events in the night sky. Stellar collisions between white dwarfs (WDs) and main-sequence (MS) stars may be detectable among such transients. Simulations will play a key role in characterizing these events and selecting targets for follow-up. We present 3D smoothed particle hydrodynamics models of dynamical interactions between a $0.6\ {\rm M}_{\odot }$ WD and 0.3, 0.6, and $1.2\ {\rm M}_{\odot }$ MS stars within globular cluster environments. Utilizing a 34-isotope nuclear network, we investigate the energetics, gas morphologies, and mass-loss properties of these collisions for different stellar mass ratios. Our models predict an overabundance of $^{13}$C, $^{15}$N, and $^{17}$O isotopes relative to solar abundances. Moreover, we find that the time-scale of the collisions is too short and maximum temperatures too low for any significant hydrogen burning or triple-alpha reactions to occur. This combined with a negligible production of elements heavier than neon may be key signatures in distinguishing these events from other transient events with similar peak bolometric luminosities ($\sim\!\! 10^{38}\!\!-\!\!10^{41}$ erg s$^{-1}$).
Human selenocysteine synthase, SEPSECS, has evolved to optimize binding of a tRNA-based substrate
Authors: Puppala Anupama K , Sosa Dylan , Castillo Suchkou Jennifer , French Rachel L , Dobosz-Bartoszek Malgorzata , Kiernan Kaitlyn A , Simonović Miljan 
Published: October 2024

Abstract
The evolution of the genetic code to incorporate selenocysteine (Sec) enabled the development of a selenoproteome in all domains of life. O-phosphoseryl-tRNASec selenium transferase (SepSecS) catalyzes the terminal reaction of Sec synthesis on tRNASec in archaea and eukaryotes. Despite harboring four equivalent active sites, human SEPSECS binds no more than two tRNASec molecules. Though, the basis for this asymmetry remains poorly understood. In humans, an acidic, C-terminal, α-helical extension precludes additional tRNA-binding events in two of the enzyme monomers, stabilizing the SEPSECS•tRNASec complex. However, the existence of a helix exclusively in vertebrates raised questions about the evolution of the tRNA-binding mechanism in SEPSECS and the origin of its C-terminal extension. Herein, using a comparative structural and phylogenetic analysis, we show that the tRNA-binding motifs in SEPSECS are poorly conserved across species. Consequently, in contrast to mammalian SEPSECS, the archaeal ortholog cannot bind unacylated tRNASec and requires an aminoacyl group. Moreover, the C-terminal α-helix 16 is a mammalian innovation, and its absence causes aggregation of the SEPSECS•tRNASec complex at low tRNA concentrations. Altogether, we propose SEPSECS evolved a tRNASec binding mechanism as a crucial functional and structural feature, allowing for additional levels of regulation of Sec and selenoprotein synthesis.
PLAbDab-nano: a database of camelid and shark nanobodies from patents and literature
Authors: Gordon Gemma L , Greenshields-Watson Alexander , Agarwal Parth , Wong Ashley , Boyles Fergus , Hummer Alissa , Lujan Hernandez Ana G , Deane Charlotte M 
Published: October 2024

Abstract
Nanobodies are essential proteins of the adaptive immune systems of camelid and shark species, complementing conventional antibodies. Properties such as their relatively small size, solubility and high thermostability make VHH (variable heavy domain of the heavy chain) and VNAR (variable new antigen receptor) modalities a promising therapeutic format and a valuable resource for a wide range of biological applications. The volume of academic literature and patents related to nanobodies has risen significantly over the past decade. Here, we present PLAbDab-nano, a nanobody complement to the Patent and Literature Antibody Database (PLAbDab). PLAbDab-nano is a self-updating, searchable repository containing ∼5000 annotated VHH and VNAR sequences. We describe the methods used to curate the entries in PLAbDab-nano, and highlight how PLAbDab-nano could be used to design diverse libraries, as well as find sequences similar to known patented or therapeutic entries. PLAbDab-nano is freely available as a searchable web server (https://opig.stats.ox.ac.uk/webapps/plabdab-nano/).
Dynamic configuration and data security for bioinformatics cloud services with the Laniakea Dashboard
Authors: Tangaro Marco Antonio , Antonacci Marica , Donvito Giacinto , Foggetti Nadina , Mandreoli Pietro , Colombo Daniele , Pesole Graziano , Zambelli Federico 
Published: October 2024

Abstract
Technological advances in high-throughput technologies improve our ability to explore the molecular mechanisms of life. Computational infrastructures for scientific applications fulfil a critical role in harnessing this potential. However, there is an ongoing need to improve accessibility and implement robust data security technologies to allow the processing of sensitive data, particularly human genetic data. Scientific clouds have emerged as a promising solution to meet these needs. We present three components of the Laniakea software stack, initially developed to support the provision of private on-demand Galaxy instances. These components can be adopted by providers of scientific cloud services built on the INDIGO PaaS layer. The Dashboard translates configuration template files into user-friendly web interfaces, enabling the easy configuration and launch of on-demand applications. The secret management and the encryption components, integrated within the Dashboard, support the secure handling of passphrases and credentials and the deployment of block-level encrypted storage volumes for managing sensitive data in the cloud environment. By adopting these software components, scientific cloud providers can develop convenient, secure and efficient on-demand services for their users.
Updated EANO guideline on rational molecular testing of gliomas, glioneuronal, and neuronal tumors in adults for targeted therapy selection—Update 1
Authors: van den Bent Martin J , Franceschi Enrico , Touat Mehdi , French Pim J , Idbaih Ahmed , Lombardi Giuseppe , Rudà Roberta , Schweizer Leonille , Capper David , Sanson Marc , Wesseling Pieter , Weller Michael , Eoli Marica , Anghileri Elena , Bielle Franck , Euskirchen Phillipp , Geurts Marjolein , Wen Patrick Y , Preusser Matthias 
Published: October 2024

Abstract
The standard of care for adult patients with gliomas, glioneuronal, and neuronal tumors consists of combinations of surgery, radiotherapy, and chemotherapy. For many systemic cancers, targeted treatments are a major part of the standard treatment; however, the predictive significance of most of the targets for treatment in systemic cancer is less well-established in central nervous system tumors. In 2023 the European Association for NeuroOncology (EANO) Guideline Committee presented evidence-based recommendations for rational testing of molecular targets for targeted treatments. From all targets reviewed, only testing for BRAF V600E mutations was of proven clinical benefit; despite regulatory approvals for tumor agnostic treatment of NTRK gene fusions and high tumor mutational burden (TMB) for patients with adult brain tumors, the evidence of clinical benefit for adult patients was still limited. This guideline has a modular structure, allowing regular updating of individual sections and adding new ones. The present version (Update 1) presents a review of the rationale of testing for PTEN, H3F3A, MTAP, RET and IDH, and presents an update of the text on TMB high and mismatch repair deficiency. It also presents an overview of the therapeutic yield of routine next-generation sequencing for mutations and fusion detection. The Supplemental File II accompanying this version contains an in-depth review of all targets, whereas, in the main manuscript, the final recommendations of the revised and new targets are presented. Updates will be made on a regular basis.
The feasibility of a multi-site, clinic-supported, and tailored neuro-oncology exercise program
Authors: Daun Julia T , Capozzi Lauren C , Dhruva Tana , Roldan Urgoiti Gloria , McDonough Meghan H , McLaughlin Emma , Bansal Mannat , Brett Allan , Easaw Jacob C , McNeely Margaret L , Francis George J , Williamson Tanya , Danyluk Jessica , Ospina Paula A , Lesiuk Christine , de Robles Paula , Leckie Catriona , Culos-Reed S Nicole 
Published: October 2024

Abstract

Background
To address the lack of access to supportive cancer care resources, the purpose of this study was to examine the feasibility of a tailored exercise program for neuro-oncology patients.

Methods
Patients with a primary brain tumor diagnosis, &gt;18 years, and able to consent in English were recruited at 2 tertiary cancer centers in Alberta. Recruitment occurred via the electronic medical record as well as self-referral. A 12-week, tailored exercise intervention with health coaching was delivered in both one-on-one and group-based formats, either in-person or online. Measures of feasibility included tracking referral, enrollment, intervention completion and adherence, measurement completion, fidelity, participant satisfaction, and safety. Participant-reported outcomes and functional fitness were assessed at baseline and 12 weeks. Objective physical activity was tracked via a Garmin activity tracker.

Results
Recruitment occurred between April 2021–December 2022. N = 70 patients enrolled in the study and n = 51 completed the intervention. The referral rate was 31%, the enrollment rate was 66%, and intervention completion and adherence rates were 82.3% and 89.7%. At baseline and 12 weeks, measurement completion rates were 100% and 77.4% for patient-reported outcomes, and 98.4% and 75.8% for functional fitness. The average wear-time for the activity tracker was 72.8%. Fidelity of intervention delivery was 100% for exercise sessions and 87.8% for health coaching. Overall participant satisfaction was 86.5%. No major and 4 minor adverse events occurred.

Conclusions
Delivery of a tailored neuro-oncology exercise program with referral included via the electronic medical record is feasible. Future work is needed to optimize tailored programming as well as to address factors critical for implementation into standard cancer care.

Clinical Trials Registration
NCT04831190 (https://clinicaltrials.gov/ct2/show/NCT04831190).
Association of Race or Ethnicity With Extended-Spectrum Beta-Lactamase Production in Escherichia Coli: A Case Control Study
Authors: Hemenway Alice N , Biagi Mark , Murrey Timothy F , Sun Jiehuan , Osei-Badu Erica , Salazar-McKinney Adriana , Sanabria Ricardo , Al Zoubi Moamen 
Published: October 2024

Abstract

Background
There are limited and conflicting data regarding the impact of race or ethnicity on the rate of gram-negative antimicrobial resistance. This study was performed to determine whether there is a difference in extended-spectrum beta-lactamase (ESBL) Escherichia coli infection or colonization in minoritized patients when compared to White patients from a diverse US Midwestern city.

Methods
A case control study was performed, with controls with non-ESBL E. coli matched 1:1 to patients with ESBL-producing E coli based on age, sex, and ZIP code. A variety of other evidence-based factors for ESBL Enterobacterales infection and colonization were collected via chart review. Multivariate conditional logistic regression assessed the odds of minoritized patients as compared to White patients, while controlling for other common risk factors for ESBL Enterobacterales.

Results
A total of 364 matched pairs were included in the analysis. Females were the majority of the sample (91%), with median age of 65 years. The majority of the sample identified as White (73%), followed by Hispanic (14%) and Black (10%). Urine cultures made up the majority of the cultures in the sample (97%), and this was similar between ESBL and non-ESBL groups. While controlling for these risk factors for ESBL E coli, minoritized patients had a statistically significant greater odds of ESBL-producing E coli (odds ratio, 2.53; 95% confidence interval, 1.68–3.82).

Conclusions
In our sample, which is demographically similar to the United States, minoritized patients had higher odds of ESBL-producing E coli. Further research on the drivers for this disparity is needed.