bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineered Mycobacteriophage TM4::GeNL Rapidly Determines Bedaquiline, Pretomanid, Linezolid, Rifampicin, and Clofazimine Sensitivity in Mycobacterium tuberculosis Clinical Isolates
Authors: Rajagopalan Saranathan , Rourke Amy K , Asare Emmanuel , Kohlerschmidt Donna J , Das Lahari , Ngema Senamile L , Mulholland Claire V , Vilchèze Catherine , Mahalingam Vaishnavi , Moodley Sashen , Truebody Barry , Mackenzie Jared , Steyn Adrie J C , Perumal Rubeshan , Berney Michael , Larsen Michelle H , O’Donnell Max R , Escuyer Vincent E , Jacobs William R 
Published: October 2024

Abstract

Background
Drug-resistant tuberculosis is a growing public health threat, and early characterization of the resistance phenotype is essential for guiding treatment and mitigating the high mortality associated with the disease. However, the slow growth rate of Mycobacterium tuberculosis, the causative agent of tuberculosis, necessitates several weeks for conventional culture-dependent drug susceptibility testing (DST). In addition, there are no widely available molecular diagnostic assays for evaluating resistance to newer tuberculosis drugs or drugs with complex resistance mechanisms.

Methods
We have developed a luciferase-based reporter mycobacteriophage assay that can determine drug resistance within 48 hours. We engineered the TM4 mycobacteriophage to express green enhanced nanoluciferase (GeNL) cassette and optimized DST for bedaquiline, pretomanid, linezolid, clofazimine, and rifampicin using clinical M. tuberculosis isolates.

Results
To assess the feasibility of this assay, we conducted a proof-of-principle study using 53 clinical M. tuberculosis isolates. TM4::GeNL phage DST effectively distinguished between sensitive and resistant isolates for bedaquiline and rifampicin at a concentration of 0.125 μg/mL. Optimal differentiation between sensitive and resistant isolates for pretomanid, clofazimine, and linezolid was achieved at concentrations of 0.5 μg/mL, 0.25 μg/mL, and 1 μg/mL, respectively. Additionally, TM4::GeNL DST identified low-level rifampicin resistance in clinical isolates even though they were classified as sensitive by Mycobacteria Growth Indicator Tube DST.

Conclusions
TM4::GeNL reporter phage DST offers a rapid method to identify M. tuberculosis drug resistance, including resistance to newer tuberculosis drugs.
To assess the availability of antibiotics for online sale and comparison of e-pharmacies on key characteristics influencing safe and rational use of antibiotics: an exploratory analysis
Authors: Kaur Puneet , Kaur Navjot , Singh Jasbir , Kaur Jasmeen 
Published: October 2024

Abstract

Background
Growing antimicrobial resistance represents serious public health threat. With the increasing presence of online/e-pharmacies in India, public access to medicines has increased. Easy access coupled with lack of adequate and authentic drug information can undermine rational antibiotic use.

Objectives
The present study aimed at exploring the availability of antibiotics for online sale and comparing the e-pharmacies on key characteristics influencing safe and rational use of antibiotics.

Methods
A cross-sectional study was conducted over a period of 3 months using the websites of 10 popular e-pharmacies in India. Availability of antibiotics for online sale was assessed in context of the National List of Essential Medicines, 2022 and WHO-AWaRe (Access, Watch, Reserve) categories. Three separate questionnaires were developed to extract and compare relevant information from e-pharmacies pertaining to their safety and authenticity (in light of the expected standards laid down in draft e-pharmacy rules, 2018), availability of drug product and consumer awareness information for promoting prudent antibiotic use. Data were summarized using descriptive statistics.

Results
Out of the 17 antibiotics studied; antibiotics belonging to all WHO-AWaRe categories i.e. Access (83.33%), Watch (88.33%) and Reserve (78%) groups were available through e-pharmacies. Wide variation exists among the e-pharmacies regarding compliance to studied parameters under three questionnaires.

Conclusions
Increased access to Watch and Reserve groups of antibiotics can translate into antibiotic misuse. It is therefore crucial that the regulatory gaps concerning e-pharmacies are addressed urgently and consumers are educated regarding safe and rational use of antibiotics.
Double designers: detection of bromazolam and metonitazene in postmortem casework
Authors: Van Cleve Danielle , Liebl Mackenzie , Kazaryan Ani 
Published: October 2024

Abstract
The identification of novel psychoactive substances (NPSs) in casework at the Los Angeles County Department of Medical Examiner (LACDME) is constantly evolving. The case detailed herein marks the first detection of metonitazene (MTZ) in forensic casework at the LACDME, which occurred in August 2023. Furthermore, bromazolam was found in the decedent’s system and both substances were identified in drug evidence collected at the death scene. No other drugs were detected and the manner and cause of death were determined as accidental due to effects of bromazolam and MTZ. The concentrations detected were 1.6 ng/mL and 4.4 ng/mL of MTZ in the jugular blood and femoral blood, respectively, and 93 ng/mL of bromazolam in the femoral blood. Constraints in screening techniques conducted by toxicology laboratories create challenges in which numerous NPSs available on the illicit drug market can go undetected. Even if labs detect an NPS in their screening methodology, confirmation methods might not cover every NPS, given the impracticality of labs keeping pace with validations as new NPSs emerge in casework. The significance of testing medical evidence collected at death scenes by drug chemistry analysis becomes crucial when initial toxicology results are negative. In cases where there is evidence of potential drug paraphernalia, this is especially true as it can be pivotal in determining the cause and manner of death.
Price Setting and Price Stickiness: A Behavioral Foundation of Inaction Bands
Authors: Angelis Georgios 
Published: October 2024

Abstract
This paper puts forward a behavioral theory of price setting where managers maximize perceived profits following a process of mental accounting. The theory predicts a pricing rule that is similar to—but crucially different from—that of a standard menu-cost theory: There is an inaction band, but there are two rather than just one target prices, depending on whether the firm updates its price upwards or downwards. The calibrated model replicates two patterns of price microdata that standard menu-cost models have difficulty accounting for: (i) the distribution of price changes has both small and large price changes and (ii) the hazard function of price changes is downward sloping initially, that is, firms that have just recently changed their price have a higher probability of changing it again, while this probability becomes constant thereafter.
From past to future: digital methods towards artefact analysis
Authors: Harris Andrew , Cremaschi Andrea , Lim Tse Siang , De Iorio Maria , Kwa Chong Guan 
Published: October 2024

Abstract
Over the past two decades, Digital Humanities has transformed the landscape of humanities and social sciences, enabling advanced computational analysis and interpretation of extensive datasets. Notably, recent initiatives in Southeast Asia, particularly in Singapore, focus on categorizing and archiving historical data such as artwork, literature and, most notably archaeological artefacts. This study illustrates the profound potential of Digital Humanities through the application of statistical methods on two distinct artefact datasets. Specifically, we present the results of an automated minting study of mid-first millennium CE struck and cast ‘Rising Sun’ coinage from mainland Southeast Asia, while subsequently utilizing unsupervised statistical methods on 2D images of 13th–14th-century earthenware ceramics excavated from the precolonial St. Andrew’s Cathedral site in central Singapore. This research offers a comparative assessment showcasing the transformative impact of statistics-based approaches on the interpretation and analysis of diverse archaeological materials and within Digital Humanities overall.
Estimating the perceived threat threshold for acting in self-defense
Authors: Qiao Aili , John Richard S 
Published: October 2024

Abstract
We formulate the decision to engage in self-defense within a Bayesian framework and report an experiment assessing the influence of situational cues and individual difference variables on perceptions of threat and intentions to act in self-defense. US adult respondents (N = 235) read four ambiguous threat vignettes involving situations in which the respondent is alone in a high- or low-crime area and is approached by a male stranger exhibiting either high or low immediate threat cues. For each vignette, respondents indicated a probability that the stranger intends to harm and a binary intention to either engage in proactive self-defense or not. The extent to which manipulated proximal and distal cues influenced threat perception probabilities was moderated by both respondents’ gender and political orientation. Threat perception probabilities mediate the influence of both proximal and distal cues on the intention to engage in proactive self-defense. Even odds thresholds of perceived threat probability to engage in self-defense ranged from 0.62 to 0.65 across the four scenarios, suggesting that failing to react to an actual threat is perceived as two to three times more costly than that of mistaken self-defense.
Invasive fungal infections in patients with haematological malignancies at the University Hospital of Reunion Island (2018–2022): An observational study
Authors: Estagnasié Camille , Mohr Catherine , Kamus Laure , Zunic Patricia , Chirpaz Emmanuel , Moiton Marie-Pierre , Lagrange-Xelot Marie 
Published: October 2024

Abstract
Invasive fungal infections are a serious complication for haematology patients. However, there is no study on this subject in Reunion Island. The aim of this study was to estimate the incidence of invasive fungal infections in patients with haematological malignancies at the University Hospital of Reunion Island. We conducted a descriptive and ambispective study. We included any patient with haematological malignancy presenting with a putative, possible, probable, or proven invasive fungal infection, defined as per the criteria of the European Organisation for Research and Treatment of Cancer/Mycoses Study Group 2019, from January 2018 to December 2022. Data were collected from medical records and identified by ICD-10 coding and laboratory data. Eighty-nine invasive fungal infections were diagnosed in 76 patients. The 5-year incidence rate of invasive fungal infections was 1.7 per 100 person-years (95% Confidence Interval (CI) 1.3–2). Invasive aspergillosis was the most common infection (35/89, 39%), followed by invasive candidiasis (33/89, 37%), mucormycosis (7/89, 8%), and pneumocystosis (7/89, 8%). Most infections occurred in patients with acute myeloid leukaemia (32/89, 36%) and lymphoma (26/89, 29%). Six-month mortality was higher for mucormycosis (71%) than for aspergillosis (34%) and invasive candidiasis (33%). The incidence and distribution of fungal infections in haematology patients were similar to European cohorts, albeit with more mucormycosis, less pneumocystis, and a high proportion of Candida parapsilosis in candidemia.
Direct estimates of nitrogen abundance for Seyfert 2 nuclei
Authors: Dors O L , Cardaci M V , Hägele G F , Valerdi M , Ilha G S , Oliveira C B , Riffel R A , Flury S R , Arellano-Córdova K Z , Storchi-Bergmann T , Riffel R , Almeida G C , Morais I N 
Published: October 2024

ABSTRACT
We derive the nitrogen and oxygen abundances in the narrow line regions (NLRs) of a sample of 38 local ($z \: \lt \: 0.4$) Seyfert 2 nuclei. For that, we consider narrow optical emission line intensities and direct estimates of the electron temperatures ($T_{\rm e}$-method). We obtain a new theoretical expression for the nitrogen ionization correction factor [ICF($\rm N^{+}$)] for NLRs. Applying this new ICF, we unexpectedly find that NLRs and disc H ii regions exhibit similar ICF distributions. We find nitrogen abundances in the range $7.6 \: \lt \: \rm 12+log(N/H) \: \lt \: 8.6$ (mean value $8.06\pm 0.22$) or $\rm 0.4 \: \lt \: (N/N_{\odot }) \: \lt 4.7$, in the metallicity regime $8.3 \: \lt \: \rm 12+log(O/H) \: \lt \: 9.0$. Our results indicate that the dispersion in N/H abundance for a fixed O/H value in AGNs of $\sim 0.2$ dex agrees with that for disc H ii regions with similar metallicity. We show that Seyfert 2 nuclei follow a similar (N/O)–(O/H) relation to the one followed by star-forming objects. Finally, we find that active galaxies called as ..nitrogen-loud.. observed at very high redshift ($z \: \gt \: 5$) show N/O values in consonance with those derived for local NLRs. This result indicates that the main star-formation event is completed in the early evolution stages of active galaxies.
Genetic and Developmental Divergence in the Neural Crest Program between Cichlid Fish Species
Authors: Marconi Aleksandra , Vernaz Grégoire , Karunaratna Achira , Ngochera Maxon J , Durbin Richard , Santos M Emília 
Published: October 2024

Abstract
Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic program in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifier sox10 (sox10a and sox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to interspecific morphological differences, such as craniofacial structures and pigmentation. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlid sox10 paralogs, with the acquisition of a novel skeletogenic function by sox10a. When compared with teleost models zebrafish and medaka, our findings reveal that sox10 duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes—particularly those controlled by sox10s—are involved in generating morphological diversification between species and lays the groundwork for further investigations into the mechanisms underpinning vertebrate NC diversification.
Reduced expression of SMAD7 and consequent reduction of autophagy promotes endometrial stromal–myofibroblast transition and fibrosis
Authors: Yong Min , Zhou Honggui , Zeng Yuhua , Yao Yuqin , Zhu Hongtao , Hu Jianguo 
Published: October 2024

Abstract
Abnormal autophagy and the transforming growth factor-β (TGFβ)–SMAD3/7 signaling pathway play an important role in the development of intrauterine adhesions (IUAs); however, the exact underlying mechanisms remain unclear. In this study, we used IUA patient tissue and SMAD7 conditional knockout mice to detect whether SMAD7 effected IUA via regulation of autophagy and the TGFβ–SMAD3 signaling pathway. We applied a combination of techniques for the detection of p-SMAD3, SMAD7, autophagy and fibrosis-related proteins, autophagic flux, and analysis of the SMAD3 binding site. Endometrial tissue of patients with IUA exhibited lower expression levels of SMAD7. In endometrial stromal cells, silencing of SMAD7 inhibited autophagic flux, whereas overexpressed SMAD7 promoted autophagic flux. This SMAD7-mediated autophagic flux regulates the stromal–myofibroblast transition, and these phenotypes were regulated by the TGFβ–SMAD3 signaling pathway. SMAD3 directly binds to the 3ʹ-untranslated region of transcription factor EB (TFEB) and inhibits its transcription. SMAD7 promoted autophagic flux by inhibiting SMAD3, thereby promoting the expression of TFEB. In SMAD7 conditional knockout mice, the endometria showed a fibrotic phenotype. Simultaneously, autophagic flux was inhibited. On administering the autophagy activator rapamycin, this endometrial fibrosis phenotype was partially reversed. The loss of SMAD7 promotes endometrial fibrosis by inhibiting autophagic flux via the TGFβ–SMAD3 pathway. Therefore, this study reveals a potential therapeutic target for IUA.
NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids
Authors: Balduzzi Elsa , Geinguenaud Frédéric , Sordyl Dominik , Maiti Satyabrata , Farsani Masoud Amiri , Nikolaev Grigory , Arluison Véronique , Bujnicki Janusz M 
Published: October 2024

Abstract
The Nucleic Acid InfraRed Data Bank (NAIRDB) serves as a comprehensive public repository dedicated to the archival and free distribution of Fourier transform infrared (FTIR) spectral data specific to nucleic acids. This database encompasses a collection of FTIR spectra covering diverse nucleic acid molecules, including DNA, RNA, DNA/RNA hybrids and their various derivatives. NAIRDB covers details of the experimental conditions for FTIR measurements, literature links, primary sequence data, information about experimentally determined structures for related nucleic acid molecules and/or computationally modeled 3D structures. All entries undergo expert validation and curation to maintain the completeness, consistency and quality of the data. NAIRDB can be searched by similarity of nucleic acid sequences or by direct comparison of spectra. The database is open for the submission of the FTIR data for nucleic acids. NAIRDB is available at https://nairdb.genesilico.pl.
Efficacy and Safety of Dolutegravir Plus Emtricitabine vs Combined Antiretroviral Therapy for the Maintenance of HIV Suppression: Results Through Week 144 of the SIMPL’HIV Trial
Authors: Marinosci Annalisa , Sculier Delphine , Wandeler Gilles , Yerly Sabine , Stoeckle Marcel , Bernasconi Enos , Braun Dominique L , Vernazza Pietro , Cavassini Matthias , Decosterd Laurent , Günthard Huldrych F , Schmid Patrick , Limacher Andreas , Branca Mattia , Calmy Alexandra ,   the Swiss HIV Cohort Study, Sudan Rosemary , Barbieux Charlotte , Da Silva Tamara , Bernasconi-Meyer Beatrice , Metzner Karin J 
Published: October 2024

Abstract
The SIMPL’HIV study investigated whether switching to dolutegravir (DTG) + emtricitabine (FTC) was noninferior to continuing combined antiretroviral therapy for maintaining HIV-1 suppression at 144 weeks. The study demonstrated that viral suppression, CD4 gains, adverse events, quality of life, and patient satisfaction were comparable between groups, confirming DTG + FTC’s safety and efficacy for long-term management of HIV-1 infection.
Mesonephric carcinoma of the cervix associated with ovarian serous carcinoma: a case report
Authors: Kharkhach Ayoub , Bali Asmae , Afqir Said , Bouhout Tariq , Serji Badr 
Published: October 2024

Abstract
Malignant mesonephric tumor of the uterine cervix is an extremely uncommon subtype of cervical adenocarcinoma with rare, documented cases in the literature. In this report, we present a case of 58 yo, with abdominal pain and ascites that was found to have a synchronous presence of a mesonephric adenocarcinoma of the cervix and advanced serous ovarian carcinoma on the surgical specimen. The histological study identified a tumor showing a mix of tubular and ductal growth patterns. Immunohistochemical analyses were positive for cytokeratin, vimentin, calretinin and CD10. However, the tumor cells were negative for estrogen receptor and progesterone receptor. The patient received neoadjuvant chemotherapy with a combination of carboplatin and gemcitabine followed by optimal debulking surgery and was alive after 18 months of follow up. The management of this rare case remains unclear due to the absence of management guidelines.
Transient speech impairment: a minor stroke/TIA case escaping conventional imaging methods
Authors: Khan Sheharyar H , Aljanabi Mustafa 
Published: October 2024

Abstract
This case report discusses the diagnostic challenges posed by transient ischaemic attacks (TIAs) and minor strokes presenting with atypical symptoms, focusing on a 62-year-old male presenting with isolated speech difficulties reminiscent of Broca’s aphasia. Despite initial inconclusive imaging, subsequent evaluation revealed minor periventricular changes consistent with ischaemic small vessel disease and a pre-existing lacunar infarct. The resolution of symptoms within 10 days highlights the transient nature of the event. The case underscores the importance of recognising nuanced presentations of cerebrovascular events and the necessity for standardised diagnostic criteria and assessment tools for transient speech impairments resembling Broca’s aphasia. Further research into the mechanisms underlying these transient events, utilising advanced imaging techniques, such as diffusion-weighted MRI (DWI), may be warranted to facilitate early recognition and appropriate management in clinical practice.
Improving bird abundance estimates in harvested forests with retention by limiting detection radius through sound truncation
Authors: Lebeuf-Taylor Isabelle , Knight Elly , Bayne Erin 
Published: October 2024

ABSTRACT
An inherent challenge with acoustically surveying birds is that the distance at which they can be detected depends on how far their song can be heard. We developed a distance-based sound detection space truncation method to correct for variable sampling radii due to surveying in forested or open conditions. The method was pivotal in evaluating bird responses to retention patches; without this methodological advancement, the impact of retention patches on songbird abundance was vastly underestimated. In the boreal forest, these patches of live trees are retained in regenerating harvested forests to provide ecological services for species adapted to natural disturbances. Although we did not verify our a priori assumption with ground observations, our findings suggest that limited-distance sampling better captures the effects of retention patches on bird use of harvested forests. When evaluated using unlimited distance surveys, retained trees had a negligible effect on bird abundance, whereas applying detection distance truncation highlighted the importance of retention on forest birds. We found that early to mid-seral forest songbirds benefited from retention patches, with notable increases in abundance after 10 years of regeneration. The size of retention patches, ranging from 0.1 to 1.2 ha, did not have a linear relationship with bird abundance. Instead, edge effects stemming from the configuration of these patches emerged as key determinants of abundance for the majority of the species studied. Retention patches that were nearest to unharvested forests were used the most, compared to further into harvest areas. Our research not only highlights the underestimated impact of small-scale live tree retention on forest songbirds but also introduces a significant methodological innovation in the field of acoustic monitoring.