bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community-Wide Universal HIV Test and Treat Intervention Reduces Tuberculosis Transmission in Rural Uganda: A Cluster-Randomized Trial
Authors: Marquez Carina , Atukunda Mucunguzi , Nugent Joshua , Charlebois Edwin D , Chamie Gabriel , Mwangwa Florence , Ssemmondo Emmanuel , Kironde Joel , Kabami Jane , Owaraganise Asiphas , Kakande Elijah , Ssekaynzi Bob , Abbott Rachel , Ayieko James , Ruel Theodore , Kwariisima Dalsone , Kamya Moses , Petersen Maya , Havlir Diane V , Balzer Laura B 
Published: January 2024

Abstract

Background
Human immunodeficiency virus (HIV) treatment reduces tuberculosis (TB) disease and mortality; however, the population-level impact of universal HIV-test-and-treat interventions on TB infection and transmission remain unclear.

Methods
In a sub-study nested in the SEARCH trial, a community cluster-randomized trial (NCT01864603), we assessed whether a universal HIV-test-and-treat intervention reduced population-level incident TB infection in rural Uganda. Intervention communities received annual, population-level HIV testing and patient-centered linkage. Control communities received population-level HIV testing at baseline and endline. We compared estimated incident TB infection by arms, defined by tuberculin skin test conversion in a cohort of persons aged 5 and older, adjusting for participation and predictors of infection, and accounting for clustering.

Results
Of the 32 trial communities, 9 were included, comprising 90 801 participants (43 127 intervention and 47 674 control). One-year cumulative incidence of TB infection was 16% in the intervention and 22% in the control; SEARCH reduced the population-level risk of incident TB infection by 27% (adjusted risk ratio = 0.73; 95% confidence interval [CI]: .57–.92, P = .005). In pre-specified analyses, the effect was largest among children aged 5–11 years and males.

Conclusions
A universal HIV-test-and-treat intervention reduced incident TB infection, a marker of population-level TB transmission. Investments in community-level HIV interventions have broader population-level benefits, including TB reductions.
Appraisal of amyloidosis imaging practices in the Middle East/North Africa (PYP-MENA)
Authors: Al Badarin Firas , Garashi Masoud , Aljizeeri Ahmed , Tabbalat Ramzi , Allam Adel , Bouyoucef Salah Eddine , Chauhdary Ammar 
Published: January 2024

Abstract

Aims
Whereas recommendations to optimize performance and yield of cardiac scintigraphy studies with bone-seeking tracers have been published, little is known about real-world adherence to these best practices, especially outside North America and Europe. Accordingly, we described imaging practices with this modality in a sample of nuclear laboratories in the Middle East/North Africa (MENA) region.

Methods and results
Laboratories performing radionuclide imaging for cardiac amyloidosis in the MENA region were invited to participate in this study to describe installed camera systems, type and dose of bone-avid tracers used, imaging protocols, and criteria used for study interpretation. Out of 19 invited sites, 10 completed the survey (70% government-run; 90% accredited), sites have been involved with amyloid imaging for a median of 49 months (interquartile range 24–60). The median injected dose was 20 mCi (range 10–25), and PYP was used by 90% of sites in this sample. Planar imaging with single photon emission computed tomography (SPECT) reconstruction was performed at all sites, including seven sites that performed SPECT/CT reconstruction. Lastly, only 50% of sites relied on evidence of myocardial uptake by SPECT to confirm the diagnosis of ATTR cardiomyopathy, while the rest relied on visual assessment and heart/contralateral ratio.

Conclusion
This study is the first to describe variation in imaging practices across sites in the MENA region, especially in acquisition protocols and interpretation standards. Eliminating heterogeneities identified by this study will harmonize image interpretation and reporting and will facilitate successful conduct of regional multi-centre studies.
Current management of atrial fibrillation in routine practice according to the last ESC guidelines: an EHRA physician survey—how are we dealing with controversial approaches?
Authors: Guerra Jose M , Moreno Weidmann Zoraida , Perrotta Laura , Sultan Arian , Anic Ante , Metzner Andreas , Providencia Rui , Boveda Serge , Chun Julian 
Published: January 2024

Abstract

Aims
Although guidelines for the management of atrial fibrillation (AF) are regularly published, many controversial issues remain, limiting their implementation. We aim to describe current clinical practice among European Heart Rhythm Association (EHRA) community according to last guidelines.

Methods and results
A 30 multiple-choice questionnaire covering the most controversial topics related to AF management was distributed through the EHRA Research Network, National Societies, and social media between January and February 2023. One hundred and eighty-one physicians responded the survey, 61% from university hospitals. Atrial fibrillation screening in high-risk patients is regularly performed by 57%. Only 42% has access to at least one programme aiming at diagnosing/managing comorbidities and lifestyle modifications, with marked heterogeneity between countries. Direct oral anticoagulants are the preferred antithrombotic (97%). Rhythm control is the preferred strategy in most AF phenotypes: symptomatic vs. asymptomatic paroxysmal AF (97% vs. 77%), low vs. high risk for recurrence persistent AF (90% vs. 72%), and permanent AF (20%). I-C drugs and amiodarone are preferred while dronedarone and sotalol barely used. Ablation is the first-line therapy for symptomatic paroxysmal AF (69%) and persistent AF with markers of atrial disease (57%) and is performed independently of symptoms by 15%. In persistent AF, 68% performs only pulmonary vein isolation and 32% also additional lesions.

Conclusion
There is marked heterogeneity in AF management and limited accordance to last guidelines in the EHRA community. Most of the discrepancies are related to the main controversial issues, such as those related to AF screening, management of comorbidities, pharmacological treatment, and ablation strategy.
An RNAi screen for conserved kinases that enhance microRNA activity after dauer in Caenorhabditis elegans
Authors: Roka Pun Himal , Karp Xantha 
Published: January 2024

Abstract
Gene regulation in changing environments is critical for maintaining homeostasis. Some animals undergo a stress-resistant diapause stage to withstand harsh environmental conditions encountered during development. MicroRNAs are one mechanism for regulating gene expression during and after diapause. MicroRNAs downregulate target genes posttranscriptionally through the activity of the microRNA-induced silencing complex. Argonaute is the core microRNA-induced silencing complex protein that binds to both the microRNA and to other microRNA-induced silencing complex proteins. The 2 major microRNA Argonautes in the Caenorhabditis elegans soma are ALG-1 and ALG-2, which function partially redundantly. Loss of alg-1 [alg-1(0)] causes penetrant developmental phenotypes including vulval defects and the reiteration of larval cell programs in hypodermal cells. However, these phenotypes are essentially absent if alg-1(0) animals undergo a diapause stage called dauer. Levels of the relevant microRNAs are not higher during or after dauer, suggesting that activity of the microRNA-induced silencing complex may be enhanced in this context. To identify genes that are required for alg-1(0) mutants to develop without vulval defects after dauer, we performed an RNAi screen of genes encoding conserved kinases. We focused on kinases because of their known role in modulating microRNA-induced silencing complex activity. We found RNAi knockdown of 4 kinase-encoding genes, air-2, bub-1, chk-1, and nekl-3, caused vulval defects and reiterative phenotypes in alg-1(0) mutants after dauer, and that these defects were more penetrant in an alg-1(0) background than in wild type. Our results implicate these kinases as potential regulators of microRNA-induced silencing complex activity during postdauer development in C. elegans.
Transcriptionally Active Defective HIV-1 Proviruses and Their Association With Immunological Nonresponse to Antiretroviral Therapy
Authors: Scrimieri Francesca , Bastian Estella , Smith Mindy , Rehm Catherine A , Morse Caryn , Kuruppu Janaki , McLaughlin Mary , Chang Weizhong , Sereti Irini , Kovacs Joseph A , Lane H Clifford , Imamichi Hiromi 
Published: January 2024

Abstract
A subset of antiretroviral therapy-treated persons with human immunodeficiency virus (HIV), referred to as immunological nonresponders (INRs), fails to normalize CD4+ T-cell numbers. In a case-control study involving 26 INRs (CD4 &lt; 250 cells/µL) and 25 immunological responders (IRs; CD4 ≥ 250 cells/µL), we evaluated the potential contribution of transcriptionally competent defective HIV-1 proviruses to poor CD4+ T-cell recovery. Compared to the responders, the INRs had higher levels of cell-associated HIV RNA (P = .034) and higher percentages of HLA-DR+ CD4+ T cells (P &lt; .001). While not encoding replication-competent viruses, the RNA transcripts frequently encoded HIV-1 Gag-p17 and Nef proteins. These transcripts and/or resulting proteins may activate pathway(s) leading to the immunological nonresponse phenotype.
Artifactual atomic displacements on surfaces using annular dark-field images with image simulation
Authors: Kobayashi Shunsuke , Ooe Kousuke , Nakayama Kei , Kuwabara Akihide 
Published: January 2024

Abstract
We investigated artifactual atomic displacements on a Pt (111) surface using annular dark-field (ADF) scanning transmission electron microscopy images under ideal conditions with multi-slice image simulation. Pt atomic columns on the surface exhibited artifact displacement. The bright spots shifted slightly toward the interior of the crystal, indicating that ADF imaging underestimates atomic distance measurements on the crystal surface. Multiple peak fitting is an effective method for determining the positions of bright spots and obtaining more accurate atomic positions while reducing the impact of surface-related artifacts. This is important for the measurement of interatomic distances on crystal surfaces, particularly for catalyst particles.
H i galaxy signatures in the SARAO MeerKAT galactic plane survey – II. The Local Void and its substructure
Authors: Kurapati Sushma , Kraan-Korteweg Renée C , Pisano D J , Chen Hao , Rajohnson Sambatriniaina H A , Steyn Nadia , Frank Bradley , Serra Paolo , Goedhart Sharmila , Camilo Fernando 
Published: January 2024

ABSTRACT
The Local Void is one of the nearest large voids, located at a distance of 23 Mpc. It lies largely behind the Galactic Bulge and is therefore extremely difficult to observe. We use H i 21 cm emission observations from the SARAO MeerKAT Galactic Plane Survey (SMGPS) to study the Local Void and its surroundings over the Galactic longitude range 329° &lt; ℓ &lt; 55°, Galactic latitude |b| &lt; 1.5°, and redshift cz &lt; 7500 $\rm km \, s^{-1}$. We have detected 291 galaxies to median rms sensitivity of 0.44 mJy per beam per 44 $\rm km \, s^{-1}$ channel. We find 17 galaxies deep inside the Void, 96 at the border of the Void, while the remaining 178 galaxies are in average density environments. The extent of the Void is ∼58 Mpc. It is severely underdense for the longitude range 350° &lt; ℓ &lt; 35° up to redshift z &lt; 4500 $\rm km \, s^{-1}$. The galaxies in the Void tend to have H i masses that are lower (by approximately 0.25 dex) than their average density counterparts. We find several potential candidates for small groups of galaxies, of which two groups (with 3 members and 5 members) in the Void show signs of filamentary substructure within the Void.
Two rest-frame wavelength measurements of galaxy sizes at z &lt; 1: the evolutionary effects of emerging bulges and quenched newcomers
Authors: George Angelo , Damjanov Ivana , Sawicki Marcin , Arnouts Stéphane , Desprez Guillaume , Gwyn Stephen , Picouet Vincent , Birrer Simon , Silverman John 
Published: January 2024

ABSTRACT
We analyse the size evolution of 16 000 star-forming galaxies (SFGs) and 5000 quiescent galaxies (QGs) with mass M* &gt; 109.5 M⊙ at 0.1 &lt; z &lt; 0.9 from the COSMOS field using deep CLAUDS + HSC imaging in two rest-frame wavelengths, 3000 Å (UV light) and 5000 Å (visible light). With half-light radius (Re) as proxy for size, SFGs at characteristic mass M0 = 5 × 1010 M⊙ grow by 20 per cent (30 per cent) in UV (visible) light since z ∼ 1 and the strength of their size evolution increases with stellar mass. After accounting for mass growth due to star formation, we estimate that SFGs grow by 75 per cent in all stellar mass bins and in both rest-frame wavelengths. Redder SFGs are more massive, smaller and more concentrated than bluer SFGs and the fraction of red SFGs increases with time. These results point to the emergence of bulges as the dominant mechanism for the average size growth of SFGs. We find two threshold values for the stellar mass density within central 1 kpc (Σ1): all SFGs with log Σ1 ≳ 9 are red and only QGs have log Σ1 ≳ 9.7. The size of M* = M0 QGs grows by 50 per cent (110 per cent) in the UV (visible) light. Up to $\sim 20~{{\rm per\,cent}}$ of this increase in size of massive QGs is due to newcomers (recently quenched galaxies). However, newcomers cannot explain the observed pace in the size growth of QGs; that trend has to be dominated by processes affecting individual galaxies, such as minor mergers and accretion.
Democracy’s Values and Ideals: A Duboisian Defence
Authors: Basevich Elvira 
Published: January 2024

Abstract
This essay offers a Duboisian defense of democracy’s expressive and experimental values. It argues that the expressive value of democracy supports an ideal of inclusion, whereas the experimental value of democracy supports that of innovation. One appeals to the ideal of inclusion to extend to excluded groups codified constitutional protections and to condemn white hypocrisy. The ideal of innovation, in contrast, helps one reimagine what constitutional protections should be in the first place. Drawing on Du Bois’s writings, this essay argues that the civic activities of black American counter-publics exhibited both experimental and expressive democratic values. In particular, it highlights the innovations of black women civic leaders who reimagined care work under a public conception of the common good. It concludes that counter-publics shape the asymmetric moral insight of its participants, namely, the oppressed.
The Faithfulness to Fact
Authors: Harris Kimberly Ann 
Published: January 2024

Abstract
W.E.B. Du Bois regarded social reform as a legitimate object for the scientist. This paper argues that he gave a place to nonepistemic values in scientific reasoning and, to counter the effects of scientific racism, he constructed his approach around the belief that scientists must adopt an assumption or scientific hypothesis that African Americans are human. His engagement in scientific research was a way to reform the society in which he lived, which in turn, led him to defend the faithfulness to fact as his conception of scientific objectivity. This essay examines his sophisticated theory of facts, account of the difference between the natural and human sciences, and the unique instantiation of a pragmatist theory of truth.
Bilateral hand dactylitis: An unusual presentation of the great imitator: Tuberculosis
Authors: Bulut Gökten Dilara , Yümün Kavak Fatma , Mercan Rıdvan 
Published: January 2024

ABSTRACT
The incidence of tuberculosis in developed countries has decreased over the years due to the use of effective tuberculosis drugs and improvements in socio-economic conditions. However, with the ease of global transport and increased travel to countries with high tuberculosis prevalence, the reduction in extrapulmonary tuberculosis cases has been less significant compared with the overall decrease in tuberculosis cases. Extrapulmonary tuberculosis can manifest in a variety of ways. Tuberculous dactylitis, a rare form of tuberculous osteomyelitis, was first described by Rankin in 1886. It mainly affects the short tubular bones in the hands and feet of children and is sometimes called ‘spina ventosa’. A 42-year-old male patient initially presented to an external centre reporting swelling and pain in the hand joints of one year’s duration. Despite one year of treatment with leflunomide and methylprednisolone (16 mg) and a history of methotrexate use during this period, he experienced no improvement. The patient’s condition worsened after the start of sulfasalazine. Dermatological examination was performed due to the presence of haemorrhagic crusted papules and plaques on the ventral surface of both hands. A wound culture was taken, but no bacterial growth was observed. One week after the initial evaluation, the patient complained of persistent foul-smelling nasal discharge, which led to an evaluation by the infectious disease department. At this time, the Quantiferon test was positive. Mycobacterial culture on Days 1 and 3 showed growth of the Mycobacterium tuberculosis complex.
The dimeric deubiquitinase USP28 integrates 53BP1 and MYC functions to limit DNA damage
Authors: Jin Chao , Einig Elias , Xu Wenshan , Kollampally Ravi Babu , Schlosser Andreas , Flentje Michael , Popov Nikita 
Published: January 2024

Abstract
DNA replication is a major source of endogenous DNA damage in tumor cells and a key target of cellular response to genotoxic stress. DNA replication can be deregulated by oncoproteins, such as transcription factor MYC, aberrantly activated in many human cancers. MYC is stringently regulated by the ubiquitin system - for example, ubiquitination controls recruitment of the elongation factor PAF1c, instrumental in MYC activity. Curiously, a key MYC-targeting deubiquitinase USP28 also controls cellular response to DNA damage via the mediator protein 53BP1. USP28 forms stable dimers, but the biological role of USP28 dimerization is unknown. We show here that dimerization limits USP28 activity and restricts recruitment of PAF1c by MYC. Expression of monomeric USP28 stabilizes MYC and promotes PAF1c recruitment, leading to ectopic DNA synthesis and replication-associated DNA damage. USP28 dimerization is stimulated by 53BP1, which selectively binds USP28 dimers. Genotoxic stress diminishes 53BP1–USP28 interaction, promotes disassembly of USP28 dimers and stimulates PAF1c recruitment by MYC. This triggers firing of DNA replication origins during early response to genotoxins and exacerbates DNA damage. We propose that dimerization of USP28 prevents ectopic DNA replication at transcriptionally active chromatin to maintain genome stability.
Transcriptome Analysis of Rice Root Tips Reveals Auxin, Gibberellin and Ethylene Signaling Underlying Nutritropism
Authors: Yamazaki Kiyoshi , Ohmori Yoshihiro , Takahashi Hirokazu , Toyoda Atsushi , Sato Yutaka , Nakazono Mikio , Fujiwara Toru 
Published: January 2024

Abstract
Nutritropism is a positive tropism toward nutrients in plant roots. An NH4+ gradient is a nutritropic stimulus in rice (Oryza sativa L.). When rice roots are exposed to an NH4+ gradient generated around nutrient sources, root tips bend toward and coil around the sources. The molecular mechanisms are largely unknown. Here, we analyzed the transcriptomes of the inside and outside of bending root tips exhibiting nutritropism to reveal nutritropic signal transduction. Tissues facing the nutrient sources (inside) and away (outside) were separately collected by laser microdissection. Principal component analysis revealed distinct transcriptome patterns between the two tissues. Annotations of 153 differentially expressed genes implied that auxin, gibberellin and ethylene signaling were activated differentially between the sides of the root tips under nutritropism. Exogenous application of transport and/or biosynthesis inhibitors of these phytohormones largely inhibited the nutritropism. Thus, signaling and de novo biosynthesis of the three phytohormones are necessary for nutritropism. Expression patterns of IAA genes implied that auxins accumulated more in the inside tissues, meaning that ammonium stimulus is transduced to auxin signaling in nutritropism similar to gravity stimulus in gravitropism. SAUR and expansin genes, which are known to control cell wall modification and to promote cell elongation in shoot gravitropism, were highly expressed in the inside tissues rather than the outside tissues, and our transcriptome data are unexplainable for differential elongation in root nutritropism.
A century journey of organelles research in the plant endomembrane system
Authors: Zhuang Xiaohong , Li Ruixi , Jiang Liwen 
Published: January 2024

Abstract
We are entering an exciting century in the study of the plant organelles in the endomembrane system. Over the past century, especially within the past 50 years, tremendous advancements have been made in the complex plant cell to generate a much clearer and informative picture of plant organelles, including the molecular/morphological features, dynamic/spatial behavior, and physiological functions. Importantly, all these discoveries and achievements in the identification and characterization of organelles in the endomembrane system would not have been possible without: (1) the innovations and timely applications of various state-of-art cell biology tools and technologies for organelle biology research; (2) the continuous efforts in developing and characterizing new organelle markers by the plant biology community; and (3) the landmark studies on the identification and characterization of the elusive organelles. While molecular aspects and results for individual organelles have been extensively reviewed, the development of the techniques for organelle research in plant cell biology is less appreciated. As one of the ASPB Centennial Reviews on “organelle biology,” here we aim to take a journey across a century of organelle biology research in plants by highlighting the important tools (or landmark technologies) and key scientists that contributed to visualize organelles. We then highlight the landmark studies leading to the identification and characterization of individual organelles in the plant endomembrane systems.
Ubiquitin E3 Ligase FBXO9 Regulates Pluripotency by Targeting DPPA5 for Ubiquitylation and Degradation
Authors: Swenson Samantha A , Dobish Kasidy K , Peters Hendrik C , Bea Winship C , Willow Hynes-Smith R , Caplan Mika , Wittorf Karli J , Ghosal Gargi , Buckley Shannon M 
Published: January 2024

Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have unique characteristics where they can both contribute to all three germ layers in vivo and self-renewal indefinitely in vitro. Post-translational modifications of proteins, particularly by the ubiquitin proteasome system (UPS), control cell pluripotency, self-renewal, and differentiation. A significant number of UPS members (mainly ubiquitin ligases) regulate pluripotency and influence ESC differentiation with key elements of the ESC pluripotency network (including the “master” regulators NANOG and OCT4) being controlled by ubiquitination. To further understand the role of the UPS in pluripotency, we performed an RNAi screen during induction of cellular reprogramming and have identified FBXO9 as a novel regulator of pluripotency associated protein DPPA5. Our findings indicate that FBXO9 silencing facilitates the induction of pluripotency through decreased proteasomal degradation of DPPA5. These findings identify FBXO9 as a key regulator of pluripotency.