bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recruitment of chromatin remodelers by XIST B-repeat region is variably dependent on HNRNPK
Authors: Navarro-Cobos Maria Jose , Brown Carolyn J 
Published: November 2024

Abstract
X-chromosome inactivation is triggered by the long non-coding RNA XIST, whose structure is characterized by tandem repeats that modularly recruit different proteins and chromatin remodelers. Previously, we reported that the addition of the mouse PID region to a transgene with human repeat regions A, F and E (miniXIST; 5.1 kb) enabled binding of HNRNPK and also enabled the induction of silencing and recruitment of H3K27me3, UbH2A and H4K20me1, but only partially. As the 680 bp PID region enabled so many features of inactivation, we hypothesized that augmenting the PID with more mouse or human sequences rich in CCC motifs would allow us to design a short transgene which was as effective as Full XIST. Three new transgenes using the A, F and E human domains as a backbone were tested for ability to induce silencing and heterochromatic mark recruitment. The all human-derived BhB-BhB transgene (4.9 kb) was as good as our previous miniXIST, suggesting that these domains are the human equivalent of the mouse PID region. A PID-PID transgene (5.8 kb) was not statistically different from Full XIST and could be potentially used for chromosome therapy. Adding BhB to PID (BhB-PID, 5.4 kb) had an intermediate efficacy compared to the other two transgenes, suggesting that the most important component for silencing and heterochromatic mark recruitment is the number of CCC motifs, not the species of origin. Finally, we created a heterozygous HNRNPK deletion and observed a disproportionate impact on HNRNPK and UbH2A recruitment to XIST, reflecting complex roles for the PID and HNRNPK in X-chromosome inactivation.
Genomic Analysis of Global Mycobacterium abscessus Isolates Reveals Ongoing Evolution of Drug Resistance–Associated Genes
Authors: Yang Tingting , Beach Kylie E , Zhu Chendi , Gan Mingyu , Wang Wenli , Zhou Hongjuan , Peng Lijun , Wang Shanshan , Cai Long , Li Weimin , Davis Jordan B , Cicchetti Nico , Slechta E Susan , Barker Adam , Shakir Salika M , Carey Allison F , Liu Qingyun 
Published: November 2024

Abstract
Mycobacterium abscessus (MAB) is intrinsically resistant to many antibiotics, but the evolution of acquired drug resistance is poorly understood. We analyzed published genomes of 5617 clinical MAB isolates from 20 countries and searched for signals of ongoing evolution in 35 drug resistance–associated genes. Of these, we found 14 genes that were subject to positive selection, and we identified novel mutational sites under selection. Among these, the erm(41) V80I mutation arose exclusively in strains with erm(41) 28T and affected 50.5% (1750/3465) of subsp abscessus isolates. The study provided evidence that MAB is evolving mutations in drug resistance–associated genes, and further research is needed to understand the functional consequences of these mutations.
Identification and Characterization of Ectoparasite-Borne Pathogens Through Vector and Animal Surveillance in Andean Countries, South America
Authors: Flores-Mendoza Carmen , Silva Maria , Domínguez Lillian , Bermúdez Sergio , Vásquez Gissella M 
Published: November 2024

Abstract
Infectious diseases transmitted by ectoparasites such as fleas, lice, mites, and ticks constitute a global public health problem. Tick-borne diseases are the most widely studied emerging ectoparasite-borne diseases (EBD) mainly due to their increasing incidence worldwide, including in South America. Furthermore, in Peru and neighboring Andean countries (Bolivia, Colombia, and Ecuador), surveillance reports indicate that Rickettsia species appear to be the most diverse and widely distributed ectoparasite-borne pathogens (EBP) followed by Babesia species, and with fewer species of Anaplasma, Bartonella, Borrelia, Ehrlichia, Coxiella, and Phlebovirus pathogens. Amblyomma, Dermacentor, Rhipicephalus, and Ixodes ticks were reported as the most predominant ectoparasites found infected with a diversity of EBP belonging to Rickettsia, Babesia, Anaplasma, Bartonella, and Ehrlichia species. Overall, people living in rural areas where agriculture and livestock production are their main economic means are at higher risk of EBD.
Toward understanding grapevine responses to climate change: a multi-stress and holistic approach
Authors: Martínez-Lüscher Johann , Matus José Tomás , Gomès Eric , Pascual Inmaculada 
Published: November 2024

Abstract
Recent research has extensively covered the effects of climate change factors, such as elevated CO2, rising temperatures, and water deficit on grapevine (Vitis spp.) biology. However, assessing the impacts of multiple climate change-related stresses on this crop remains complex due to interactive effects among environmental factors, and the regulatory mechanisms that underlie these. Consequently, there is a substantial discrepancy between the number of studies conducted with a single factor or two factors simultaneously, and those with a more holistic approach. Changes in crop phenology in response to temperature have been a major focus of many studies. We highlight how the impact of rising temperatures will be enhanced during specific developmental periods, such as grape ripening. However, how these shifts may result in deleterious effects on yield and quality deserves further research. Rising temperatures will most certainly continue to represent a substantial threat to viticulture due to its effects on grape phenology, composition, and crop water requirements. Nevertheless, elevated CO2 may offer some relief through increased water use efficiency, as shown in recent studies. Hormones play a major role within the repertoire of regulatory mechanisms that plants possess, with crosstalk between hormones explaining the effects of combined stresses. In fact, growth regulators can fine-tune stress responses depending on the multiple stresses present. This review focuses on the interaction of climate change factors across viticultural areas of the globe, and how multi-stress responses are mediated by abscisic acid and jasmonate, with emphasis on the intricate interconnections of signalling among different plant hormones.
Spectral Pyrometry for Practical Temperature Measurement in the TEM
Authors: Coffman D Keith , Hattar Khalid , Luo Jian , Dillon Shen 
Published: November 2024

Abstract
Recent work in ultra-high temperature in situ electron microscopy has presented the need for accurate, contact-free temperature determination at the microscale. Optical measurement based on thermal radiation (pyrometry) is an attractive solution but can be difficult to perform correctly due to effects, such as emissivity and optical transmission, that must be accounted for. Here, we present a practical guide to calibrating and using a spectral pyrometry system, including example code, using a Czerny-Turner spectrometer attached to a transmission electron microscope. Calibration can be accomplished using a thermocouple or commercial heated sample holder, after which arbitrary samples can be reliably measured for temperatures above ∼600∘C. An accuracy of 2% can be expected with the possibility of sub-second temporal resolution and sub-Kelvin temperature resolution. We then demonstrate this capability in conjunction with traditional microscopic techniques, such as diffraction-based strain measurement for thermal expansion coefficient, or live-video sintering evolution.
Attachments on Display: Music Analysis in the Public Sphere
Authors: Tan Daphne 
Published: November 2024

Abstract
In this article, I reflect on the nature of attachment within academic and public music theory. I focus on music analysis as a powerful activity that engenders attachments to musics, to methods, and often, to people. A key distinction between the scholarly and public spheres is how overtly affections and emotional commitments are expressed. Drawing first on academic writing and then turning to examples from YouTube, the podcasting world, and remarks from public music theorists, I contemplate the rewards and repercussions of putting one’s attachments on display.
PHI-base – the multi-species pathogen–host interaction database in 2025
Authors: Urban Martin , Cuzick Alayne , Seager James , Nonavinakere Nagashree , Sahoo Jahobanta , Sahu Pallavi , Iyer Vijay Laksmi , Khamari Lokanath , Martinez Manuel Carbajo , Hammond-Kosack Kim E 
Published: November 2024

Abstract
The Pathogen–Host Interactions Database (PHI-base) has, since 2005, provided manually curated genes from fungal, bacterial and protist pathogens that have been experimentally verified to have important pathogenicity, virulence and/or effector functions during different types of interactions involving human, animal, plant, invertebrate and fungal hosts. PHI-base provides phenotypic annotation and genotypic information for both native and model host interactions, including gene alterations that do not alter the phenotype of the interaction. In this article, we describe major updates to PHI-base. The latest version of PHI-base, 4.17, contains a 19% increase in genes and a 23% increase in interactions relative to version 4.12 (released September 2022). We also describe the unification of data in PHI-base 4 with the data curated from a new curation workflow (PHI-Canto), which forms the first complete release of PHI-base version 5.0. Additionally, we describe adding support for the Frictionless Data framework to PHI-base 4 datasets, new ways of sharing interaction data with the Ensembl database, an analysis of the conserved orthologous genes in PHI-base, and the increasing variety of research studies that make use of PHI-base. PHI-base version 4.17 is freely available at www.phi-base.org and PHI-base version 5.0 is freely available at phi5.phi-base.org.
Bacterial WYL domain transcriptional repressors sense single-stranded DNA to control gene expression
Authors: Blankenchip Chelsea L , Corbett Kevin D 
Published: November 2024

Abstract
Bacteria encode a wide array of immune systems to protect themselves against ubiquitous bacteriophages and foreign DNA elements. While these systems’ molecular mechanisms are becoming increasingly well known, their regulation remains poorly understood. Here, we show that an immune system-associated transcriptional repressor of the wHTH–WYL–WCX family, CapW, directly binds single-stranded DNA to sense DNA damage and activate expression of its associated immune system. We show that CapW mediates increased expression of a reporter gene in response to DNA damage in a host cell. CapW directly binds single-stranded DNA by-products of DNA repair through its WYL domain, causing a conformational change that releases the protein from double-stranded DNA. In an Escherichia coli CBASS system with an integrated capW gene, we find that CapW-mediated transcriptional activation is important for this system’s ability to prevent induction of a λ prophage. Overall, our data reveal the molecular mechanisms of WYL-domain transcriptional repressors, and provide an example of how bacteria can balance the protective benefits of carrying anti-phage immune systems against the inherent risk of these systems’ aberrant activation.
Retargeting target-directed microRNA-decay sites to highly expressed viral or cellular miRNAs
Authors: Ortega Jesus A , Liang Ziyan , Xu Junpeng Kenny , Gottwein Eva 
Published: November 2024

Abstract
MicroRNAs (miRNAs) are pervasive regulators of gene expression, necessitating the development of tools to inhibit individual miRNAs for functional studies or therapeutic targeting. Specialized base-pairing configurations between a miRNA and an RNA target site can trigger the degradation of the targeting miRNA through target-directed miRNA decay (TDMD). Previous work has identified several natural sites that induce TDMD of specific miRNAs. We explored retargeting known TDMD sites for the inhibition of heterologous miRNAs, including several encoded by Kaposi's Sarcoma-associated herpesvirus (KSHV). We focused particularly on miR-K11, a viral mimic of the oncogenic miRNA miR-155. miRNA pairing architectures based on the TDMD site in the long non-coding RNA Cyrano outperformed other retargeted sites. Cyrano-like inhibitors were specific for viral miR-K11 over cellular miR-155 and vice versa. Lentiviral delivery of a Cyrano-like miR-K11 inhibitor into KSHV-transformed primary effusion lymphoma (PEL) cells impaired their viability, showing that miR-K11 promotes KSHV-dependent PEL cell survival. Surprisingly, inactivation of ZSWIM8, a key mediator of TDMD, did not substantially affect miRNA inhibition by retargeted Cyrano-based inhibitors in 293T or PEL cells. Together, our results demonstrate the feasibility of retargeting natural TDMD sites to highly expressed viral or cellular miRNAs and further define features of effective encoded miRNA inhibitors.
Perioperative Extracorporeal Cardiopulmonary Resuscitation in Adults: A Single-center Retrospective Review and Analysis
Authors: Kapoor Ashie , Wolfe Michael W. , Chen Weiting , Benharash Peyman , Gudzenko Vadim 
Published: November 2024

Background:
Extracorporeal cardiopulmonary resuscitation (CPR) for refractory in-hospital cardiac arrest has been associated with improved survival compared with conventional CPR. Perioperative patients represent a unique cohort of the inpatient population. This study aims to describe and analyze the characteristics and outcomes of patients who received extracorporeal CPR for perioperative cardiac arrest.

Methods:
A single-center retrospective review of perioperative extracorporeal CPR in adults from January 2015 to August 2022 was performed. Patient demographics, cardiac arrest variables, and outcome data were obtained and analyzed. The primary study outcome was survival with favorable neurologic outcome.

Results:
A total of 33 patients received extracorporeal CPR for perioperative cardiac arrest. Of the 33 patients, 24 (73%) had a cardiac arrest in the cardiac catheterization laboratory, while 9 (27%) had a cardiac arrest in the operating room or interventional radiology suite. Survival to discharge was 57.6%, of whom 17 (89.5%) had neurologically favorable outcomes with cerebral performance category scores of 1 or 2 at discharge. The mean total CPR time was significantly lower in the survivor group than in the nonsurvivor group (16.5 vs. 25.0 min; P < 0.05). Survivors had significantly lower lactate levels (73 mg/dl vs. 115 mg/dl; P = 0.005) and higher pH levels (7.17 vs. 7.03; P = 0.005) compared with nonsurvivors.

Conclusions:
The use of extracorporeal CPR for adults with perioperative cardiac arrest can be associated with excellent survival with neurologically favorable outcomes in carefully selected patients. Longer CPR time, higher lactate levels, and lower pH were associated with increased mortality. Given the small sample size, no other prognostic factors were identified, although certain trends were detected between survival groups.
Minimally Invasive Arthroscopic–Assisted Treatment for Isolated Scaphoid Fossa Die Punch Nascent Malunion
Authors: Marcovici Lucian Lior , Greco Alessandro , Muscatiello Antonio Luca , Chiossi Beatrice , Pagnotta Alessia 
Published: November 2024

A die punch fracture is an intra-articular fracture of the distal radius characterized by a localized depression of the articular surface, typically occurring in the lunate fossa. Misdiagnosis or incorrect management can lead to articular malunion. While die punch fractures in the scaphoid fossa are less common, their nascent malunions pose significant treatment challenges. Traditionally, these fractures are treated with an open dorsal and volar approach, combined with osteotomy and internal fixation. Arthroscopic-assisted osteotomy has emerged as a promising technique due to its precision and minimally invasive nature. We present a new arthroscopic assisted minimally invasive technique for treating isolated dislocated die punch fracture nascent malunion of the scaphoid fossa. We treated an isolated scaphoid die punch nascent malunion, with a 5 mm joint surface depression. Using a 3-4 portal and a 30-degree curved mini osteotome, we performed an intra-articular osteotomy of the fragment. A small 2 cm skin incision over the Lister tubercle and a 1 cm bone window facilitated the introduction of a 30-degree curved curette to elevate and anatomically reduce the fragment under arthroscopic guidance. Definitive fixation was achieved with 3 K-wires. Postoperative x-rays at 6 weeks show complete fracture consolidation, confirmed by a subsequent computed tomography scan. At 3 months, patients demonstrated satisfactory clinical recovery with wrist range of motion and grip strength equal to the contralateral wrist, returning to normal activities.
This technique is feasible and safe, minimizing soft tissue damage, preserving proprioception and vascularity, and enabling faster recovery.
Improving Executive Function in Children and Adolescents with Cognitive-Engaging Physical Activity: A Systematic Review and Multilevel Meta-Analysis
Authors: Teng Gesi , Xia Haishuo , Li Qing , Chen Antao 
Published: November 2024

ABSTRACT:
Executive function (EF) development is vital for children and adolescents, with physical activity (PA) playing a key role in its enhancement. Through a systematic review and multilevel meta-analysis, this study investigates the effectiveness of cognitively engaging physical activity (CEPA) over traditional PA in fostering EF in children and adolescents. The research involved 1671 participants across 15 studies to determine if CEPA is superior to PA in enhancing EF and to analyze interventions and dose-response effects. Results demonstrated that CEPA had a more pronounced impact on EF development compared with PA, with a Hedges' g of 0.50 (95% confidence interval, 0.10–0.48), although potentially overestimated due to small-study effects and publication bias. Subgroup analyses did not find notable differences in effectiveness among various intervention types. The most substantial effect was observed with 45-minute interventions, while frequencies less than twice weekly and durations beyond 12 weeks were less effective. These findings suggest that CEPA could be a more efficacious method for advancing EF in youth, indicating a need for larger-scale randomized controlled trial (RCTs) to confirm the results and more accurately estimate their magnitude.
Selective Mutism in the Context of Autism and Bilingualism
Authors: Carroll Bridgette , Bordes Edgar Veronica , Bar Sari H. , Call Cynthia R. , Nyp Sarah S. 
Published: November 2024

CASE:
Juan is a 5-year-old boy who has been followed by a developmental-behavioral pediatrician and pediatric neuropsychologist since being diagnosed with language delay and autism spectrum disorder at age 2 years. He is otherwise healthy and was born at term after a healthy pregnancy. His primary language is Spanish, and he has minimal interactions in English. His first words were at 20 months; they were not functional but rather words related to his interests such as “train.” He began using 2 to 3-word phrases shortly after but only to request needs. He began speaking in complete sentences at age 4 years.
A neuropsychological evaluation was conducted at age 2 years during which Juan demonstrated repetitive behaviors such as hand-flapping, toe-walking, body rocking, and head banging. He displayed sensory seeking behaviors such as rubbing items on his face and close visual inspection. He did not respond to his name and his use of eye contact was inconsistent. He demonstrated rigidity and difficulty transitioning between activities. He did not engage in social reciprocity, and his facial expressions were limited. Minimal spontaneous language was observed, and expressive language largely consisted of echolalia in both languages. Juan was diagnosed with autism spectrum disorder and applied behavior analysis, speech and language therapy, and occupational therapy were recommended.
Developmental-behavioral follow-up over the next 2 years noted improvements in behavior, transitions, and social interactions. He participated in early childhood intervention and early childhood special education with significant advances for speech and language in English and Spanish, demonstrating a large vocabulary. At 4 years, parents noted Juan to have reluctance to speak in English. He stopped speaking in English entirely for 3 weeks, though he continued to speak in Spanish. When he resumed speaking in English, it was only with people he knew well (e.g., parents, teachers, babysitter). In clinic, he did not speak to the English-speaking developmental-behavioral pediatrician but spoke in short sentences to the Spanish-speaking neuropsychologist.
A repeat neuropsychological evaluation completed at age 5 years revealed that Juan had stopped speaking in English completely, even among those previously deemed “safe.” Results were consistent with average cognitive abilities with a strength in verbal skills. Juan's single-word vocabulary in Spanish was exceptionally high. He did not provide expressive responses in English, but his receptive English vocabulary was high average. He responded to English language with nonverbal gestures or spoken language in Spanish. Parents reported Juan to display increased anxiety accompanied by extreme school refusal, behavioral difficulties, and reluctance to leave the home.
Given this information, what are your diagnostic considerations and treatment recommendations?
Subclinical target organ damage in a sample of children and adolescents with solitary functioning kidney. A pilot study
Authors: Tagetti Angela , Cattazzo Filippo , Marcon Denise , Romano Simone , Giontella Alice , Bortolotti Stefano , Minuz Pietro , Pecoraro Luca , Brugnara Milena , Fava Cristiano 
Published: November 2024

Background:
Patients with solitary functioning kidney appear to be exposed to an increased cardiovascular risk. This study aimed to evaluate the impact of peripheral and central blood pressure on subclinical cardiovascular organ damage in a sample of children and adolescents with solitary functioning kidney.

Methods:
Carotid ultrasonography was performed to measure the carotid intima-media thickness (cIMT) and the carotid distensibility coefficient. The carotid-femoral pulse wave velocity (PWV) was assessed by tonometry. Cardiac mass and remodeling were estimated using transthoracic echocardiography. Central and peripheral (both office and 24-h ambulatory) BP measurements were collected.

Results:
Forty-four patients were included. Eighteen subjects (45%) were hypertensive as assessed by 24-h ABPM, with a prevalence of masked hypertension of 43%. Twenty-three subjects (52%) had an increased cIMT, while 2 and 3 patients (5% and 7%) demonstrated an impaired carotid distensibility coefficient and PWV, respectively. Nineteen subjects (43%) showed concentric cardiac remodeling. Central systolic blood pressure (cSBP) correlated with cIMT (r = 0.35) and left ventricular mass index (LVMi) (r = 0.32) demonstrating a positive independent association with an increased cIMT (odds ratio 1.14, 95% confidence interval 1.01–1.29) in multivariate regression analysis.

Conclusion:
Children and adolescents with solitary functioning kidney exhibited a high prevalence of masked hypertension and subclinical cardiovascular organ damage. These findings support the use of 24-h ABPM to identify patients with a higher cardiovascular risk who would benefit from hypertension treatment and closer monitoring during growth and into adulthood. Additionally, cSBP measurement should be considered as part of a more detailed cardiovascular risk assessment in these patients.