bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candida parapsilosis: A systematic review to inform the World Health Organization fungal priority pathogens list
Authors: Asogan Mrudhula , Kim Hannah Yejin , Kidd Sarah , Alastruey-Izquierdo Ana , Govender Nelesh P , Dao Aiken , Shin Jong-Hee , Heim Jutta , Ford Nathan Paul , Gigante Valeria , Sati Hatim , Morrissey C Orla , Alffenaar Jan-Willem , Beardsley Justin 
Published: June 2024

Abstract
Candida parapsilosis is globally distributed and recognised for causing an increasing proportion of invasive Candida infections. It is associated with high crude mortality in all age groups. It has been particularly associated with nosocomial outbreaks, particularly in association with the use of invasive medical devices such as central venous catheters. Candida parapsilosis is one of the pathogens considered in the WHO priority pathogens list, and this review was conducted to inform the ranking of the pathogen in the list. In this systematic review, we searched PubMed and Web of Science to find studies between 2011 and 2021 reporting on the following criteria for C. parapsilosis infections: mortality, morbidity (hospitalisation and disability), drug resistance, preventability, yearly incidence, and distribution/emergence. We identified 336 potentially relevant papers, of which 51 were included in the analyses. The included studies confirmed high mortality rates, ranging from 17.5% to 46.8%. Data on disability and sequelae were sparse. Many reports highlighted concerns with azole resistance, with resistance rates of &gt;10% described in some regions. Annual incidence rates were relatively poorly described, although there was clear evidence that the proportion of candidaemia cases caused by C. parapsilosis increased over time. While this review summarises current data on C.parapsilosis, there remains an urgent need for ongoing research and surveillance to fully understand and manage this increasingly important pathogen.
Histoplasmosis: A systematic review to inform the World Health Organization of a fungal priority pathogens list
Authors: Dao Aiken , Kim Hannah Yejin , Halliday Catriona L , Oladele Rita , Rickerts Volker , Govender MMed Nelesh P , Shin Jong-Hee , Heim Jutta , Ford Nathan Paul , Nahrgang Saskia Andrea , Gigante Valeria , Beardsley Justin , Sati Hatim , Morrissey C Orla , Alffenaar Jan-Willem , Alastruey-Izquierdo Ana 
Published: June 2024

AbstractHistoplasmosis, a significant mycosis primarily prevalent in Africa, North and South America, with emerging reports globally, poses notable health challenges, particularly in immunocompromised individuals such as people living with HIV/AIDS and organ transplant recipients. This systematic review, aimed at informing the World Health Organization’s Fungal Priority Pathogens List, critically examines literature from 2011 to 2021 using PubMed and Web of Science, focusing on the incidence, mortality, morbidity, antifungal resistance, preventability, and distribution of Histoplasma. We also found a high prevalence (22%–44%) in people living with HIV, with mortality rates ranging from 21% to 53%. Despite limited data, the prevalence of histoplasmosis seems stable, with lower estimates in Europe. Complications such as central nervous system disease, pulmonary issues, and lymphoedema due to granuloma or sclerosis are noted, though their burden remains uncertain. Antifungal susceptibility varies, particularly against fluconazole (MIC: ≥32 mg/l) and caspofungin (MICs: 4–32 mg/l), while resistance to amphotericin B (MIC: 0.125–0.16 mg/l), itraconazole (MICs: 0.004–0.125 mg/l), and voriconazole (MICs: 0.004–0.125 mg/l) remains low. This review identifies critical knowledge gaps, underlining the need for robust, globally representative surveillance systems to better understand and combat this fungal threat.
Eumycetoma causative agents: A systematic review to inform the World Health Organization priority list of fungal pathogens
Authors: Clark Julia E , Kim Hannah Yejin , van de Sande Wendy W J , McMullan Brendan , Verweij Paul , Alastruey-Izquierdo Ana , Chakrabarti Arunaloke , Harrison Thomas S , Bongomin Felix , Hay Roderick J , Oladele Rita , Heim Jutta , Beyer Peter , Galas Marcelo , Siswanto Siswanto , Dagne Daniel Argaw , Roitberg Felipe , Gigante Valeria , Beardsley Justin , Sati Hatim , Alffenaar Jan-Willem , Morrissey C Orla 
Published: June 2024

Abstract
The World Health Organization, in response to the growing burden of fungal disease, established a process to develop a fungal priority pathogens list. This systematic review aimed to evaluate the epidemiology and impact of eumycetoma. PubMed and Web of Science were searched to identify studies published between 1 January 2011 and 19 February 2021. Studies reporting on mortality, inpatient care, complications and sequelae, antifungal susceptibility, risk factors, preventability, annual incidence, global distribution, and emergence during the study time frames were selected. Overall, 14 studies were eligible for inclusion. Morbidity was frequent with moderate to severe impairment of quality of life in 60.3%, amputation in up to 38.5%, and recurrent or long-term disease in 31.8%–73.5% of patients. Potential risk factors included male gender (56.6%–79.6%), younger age (11–30 years; 64%), and farming occupation (62.1%–69.7%). Mycetoma was predominantly reported in Sudan, particularly in central Sudan (37%–76.6% of cases). An annual incidence of 0.1/100 000 persons and 0.32/100  000 persons/decade was reported in the Philippines and Uganda, respectively. In Uganda, a decline in incidence from 3.37 to 0.32/100  000 persons between two consecutive 10-year periods (2000–2009 and 2010–2019) was detected. A community-based, multi-pronged prevention programme was associated with a reduction in amputation rates from 62.8% to 11.9%. With the pre-specified criteria, no studies of antifungal drug susceptibility, mortality, and hospital lengths of stay were identified. Future research should include larger cohort studies, greater drug susceptibility testing, and global surveillance to develop evidence-based treatment guidelines and to determine more accurately the incidence and trends over time.
Testing the near-far connection with FIRE simulations: inferring the stellar mass function of the proto-Local Group at z &gt; 6 using the fossil record of present-day galaxies
Authors: Gandhi Pratik J , Wetzel Andrew , Boylan-Kolchin Michael , Sanderson Robyn E , Savino Alessandro , Weisz Daniel R , Tollerud Erik J , Sun Guochao , Faucher-Giguère Claude-André 
Published: June 2024

ABSTRACT
The shape of the low-mass (faint) end of the galaxy stellar mass function (SMF) or ultraviolet luminosity function (UVLF) at $z \gtrsim 6$ is an open question for understanding which galaxies primarily drove cosmic reionization. Resolved photometry of Local Group low-mass galaxies allows us to reconstruct their star formation histories, stellar masses, and UV luminosities at early times, and this fossil record provides a powerful ‘near-far’ technique for studying the reionization-era SMF/UVLF, probing orders of magnitude lower in mass than direct HST/JWST observations. Using 882 low-mass ($M_{\rm star}\lesssim 10^{9}\, \rm {M_\odot }$) galaxies across 11 Milky Way (MW)- and Local Group-analogue environments from the FIRE-2 cosmological baryonic zoom-in simulations, we characterize their progenitors at $z=6\!-\!9$, the mergers/disruption of those progenitors over time, and how well their present-day fossil record traces the high-redshift SMF. A present-day galaxy with $M_{\rm star}\sim 10^5\, \rm {M_\odot }$ ($\sim 10^9\, \rm {M_\odot }$) had $\approx 1$ ($\approx 30$) progenitors at $z\approx 7$, and its main progenitor comprised $\approx 100~{{\ \rm per\ cent}}$ ($\approx 10~{{\ \rm per\ cent}}$) of the total stellar mass of all its progenitors at $z\approx 7$. We show that although only $\sim 15~{{\ \rm per\ cent}}$ of the early population of low-mass galaxies survives to present day, the fossil record of surviving Local Group galaxies accurately traces the low-mass slope of the SMF at $z \sim 6 \!-\! 9$. We find no obvious mass dependence to the mergers and accretion, and show that applying this reconstruction technique to just low-mass galaxies at $z = 0$ and not the MW/M31 hosts correctly recovers the slope of the SMF down to $M_{\rm star} \sim 10^{4.5}\, \rm {{\rm M}_{\odot }}$ at $z \gtrsim 6$. Thus, we validate the ‘near-far’ approach as an unbiased tool for probing low-mass reionization-era galaxies.
Measuring the substructure mass power spectrum of 23 SLACS strong galaxy–galaxy lenses with convolutional neural networks
Authors: Fagin Joshua , Vernardos Georgios , Tsagkatakis Grigorios , Pantazis Yannis , Shajib Anowar J , O’Dowd Matthew 
Published: June 2024

ABSTRACT
Strong gravitational lensing can be used as a tool for constraining the substructure in the mass distribution of galaxies. In this study we investigate the power spectrum of dark matter perturbations in a population of 23 Hubble Space Telescope images of strong galaxy–galaxy lenses selected from The Sloan Lens ACS (SLACS) survey. We model the dark matter substructure as a Gaussian random field perturbation on a smooth lens mass potential, characterized by power-law statistics. We expand upon the previously developed machine learning framework to predict the power-law statistics by using a convolutional neural network (CNN) that accounts for both epistemic and aleatoric uncertainties. For the training sets, we use the smooth lens mass potentials and reconstructed source galaxies that have been previously modelled through traditional fits of analytical and shapelet profiles as a starting point. We train three CNNs with different training set: the first using standard data augmentation on the best-fitting reconstructed sources, the second using different reconstructed sources spaced throughout the posterior distribution, and the third using a combination of the two data sets. We apply the trained CNNs to the SLACS data and find agreement in their predictions. Our results suggest a significant substructure perturbation favouring a high frequency power spectrum across our lens population.
Systematic comparison of neural networks used in discovering strong gravitational lenses
Authors: More Anupreeta , Cañameras Raoul , Jaelani Anton T , Shu Yiping , Ishida Yuichiro , Wong Kenneth C , Inoue Kaiki Taro , Schuldt Stefan , Sonnenfeld Alessandro 
Published: June 2024

ABSTRACT
Efficient algorithms are being developed to search for strong gravitational lens systems owing to increasing large imaging surveys. Neural networks have been successfully used to discover galaxy-scale lens systems in imaging surveys such as the Kilo Degree Survey, Hyper-Suprime Cam (HSC) Survey, and Dark Energy Survey over the last few years. Thus, it has become imperative to understand how some of these networks compare, their strengths and the role of the training data sets which are essential in supervised learning algorithms used commonly in neural networks. In this work, we present the first-of-its-kind systematic comparison and benchmarking of networks from four teams that have analysed the HSC Survey data. Each team has designed their training samples and developed neural networks independently but coordinated a priori in reserving specific data sets strictly for test purposes. The test sample consists of mock lenses, real (candidate) lenses, and real non-lenses gathered from various sources to benchmark and characterize the performance of each of the network. While each team’s network performed much better on their own constructed test samples compared to those from others, all networks performed comparable on the test sample with real (candidate) lenses and non-lenses. We also investigate the impact of swapping the training samples among the teams while retaining the same network architecture. We find that this resulted in improved performance for some networks. These results have direct implications on measures to be taken for lens searches with upcoming imaging surveys such as the Rubin-Legacy Survey of Space and Time, Roman, and Euclid.
ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer
Authors: Qian Chen , Yang Qian , Rotinen Mirja , Huang Rongrong , Kim Hyoyoung , Gallent Brad , Yan Yiwu , Cadaneanu Radu M , Zhang Baohui , Kaochar Salma , Freedland Stephen J , Posadas Edwin M , Ellis Leigh , Di Vizio Dolores , Morrissey Colm , Nelson Peter S , Brady Lauren , Murali Ramachandran , Campbell Moray J , Yang Wei , Knudsen Beatrice S , Mostaghel Elahe A , Ye Huihui , Garraway Isla P , You Sungyong , Freeman Michael R 
Published: June 2024

Abstract
Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 gene targets include the glucocorticoid receptor (GR; NR3C1) and the NE splicing factor SRRM4, which are key drivers of lineage plasticity. Thus, OC2, despite its previously described NEPC driver function, can indirectly activate a portion of the AR cistrome through epigenetic activation of GR. Mechanisms by which OC2 regulates gene expression include promoter binding, enhancement of genome-wide chromatin accessibility, and super-enhancer reprogramming. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC and support enhanced efforts to therapeutically target OC2 as a means of suppressing treatment-resistant disease.
Functional analysis of protein interactions using coupled bi-fluorescence complementation/GFP nanobody techniques
Authors: Miyake Tetsuaki , McDermott John C 
Published: June 2024

Abstract
Transcription factors (TFs) form homo- or hetero-dimeric DNA binding complexes along with associated co-regulators that can have transcriptional repressor or activator functions. Defining the specific composition of the complexes is therefore key to understanding their biological role. Here, we utilized bimolecular fluorescence complementation (BiFC) to visualize the formation of defined TF dimers and associated co-regulators derived from the activator protein-1 (AP-1) and myocyte enhancer factor 2 (MEF2) families. Firstly, BiFC signals were observed in cells co-expressing TFs tagged with complimentary combinations of the split fluorescent protein, demonstrating the engineered formation of defined dimer complexes. Next, we applied this approach and determined that defined AP-1 dimers localized at discrete sub-nuclear locations. Subsequently, a combination of BiFC coupled with GFP binding peptide (GBP)-nanotrap allowed observation of protein-protein interactions between a co-regulator, HDAC4, and defined BiFC-MEF2 engineered dimers. To determine transactivation properties of defined TF dimers in a cellular system, the Gal4-DNA binding domain fused to GBP was utilized to assess the transcriptional properties of the BiFC-TF dimers using a generically applicable Gal4/UAS luciferase reporter gene assay system. Here, we report efficacy of a BiFC/GBP-nanobody approach that allows engineering, visualization, and functional analysis of defined TF dimers.
Swarming caddisflies in the mid-cretaceous
Authors: Wang Jiajia , Engel Michael S , Zhang Weiting , Shih Chungkun , Qiu Rui , Ren Dong 
Published: June 2024

ABSTRACT
Swarming, as a special form of mating aggregation, is most noteworthy in insects of the orders Ephemeroptera, Diptera, and Trichoptera. Swarming in extant trichopterans is well understood in terms of sex composition, specific mating behaviors, and functional morphological specializations of adults, but an exploration of the evolution of such aggregative behaviors is hampered by the dearth of available examples from the fossil record as well as the ability to reliably distinguish the few gatherings as the result of swarming relative to other taphonomic or behavioral factors. Herein we describe five new fossil species of caddisflies preserved in mid-Cretaceous amber from Myanmar, all preserved as large aggregations. Monospecific aggregations of these five new species can be positively identified as swarms based on morphological traits of wing shape, as well as the presence of particular forms of sexual dimorphism. Results of a phylogenetic reconstruction of both molecular and morphological data as well as ancestral-trait reconstructions and tip-dating analyses indicate that swarming was likely present in the Triassic as a feature of the trichopteran groundplan. Since most Mesozoic insectivorous predators were diurnal based on morphological evidence, largely nocturnal caddisflies would have been freed from such pressures. The phylogeny also shows a correlation between the rise of nocturnal bat predators from the Paleocene or early Eocene and the repeated loss of swarming from various clades of caddisflies, revealing the potential impact of bat predation on reshaping the behavioral landscape of Trichoptera during the Cenozoic.
“Keep it a secret”: Leaked Documents Suggest Philip Morris International, and Its Japanese Affiliate, Continue to Exploit Science for Profit
Authors: Braznell Sophie , Laurence Louis , Fitzpatrick Iona , Gilmore Anna B 
Published: June 2024

Abstract

Introduction
The tobacco industry has a long history of manipulating science to conceal the harms of its products. As part of its proclaimed transformation, the world’s largest tobacco company, Philip Morris International (PMI), states it conducts “transparent science.” This paper uses recently leaked documents from PMI and its Japanese affiliate, Philip Morris Japan (PMJ), to examine its contemporary scientific practices.

Aims and Methods
Twenty-four documents dating 2012 through 2020 available from the Truth Tobacco Industry Documents Library were examined using Forster’s hermeneutic approach to analyzing corporate documentation. Thematic analysis using the Science for Profit Model was conducted to assess whether PMI and PMJ employed known corporate strategies to influence science in their interests.

Results
PMJ contracted third-party external research organization, CMIC, to covertly fund a study on smoking cessation conducted by Kyoto University academics. No public record of PMJ’s funding or involvement in this study was found. PMJ paid life sciences consultancy, FTI-Innovations, ¥3 000 000 (approx. £20 000) a month between 2014 and 2019 to undertake extensive science-adjacent work, including building relationships with key scientific opinion leaders and using academic events to promote PMI’s science, products and messaging. FTI-Innovation’s work was hidden internally and externally. These activities resemble known strategies to influence the conduct, publication and reach of science, and conceal scientific activities.

Conclusions
The documents reveal PMI and PMJ’s recent activities mirror past practices to manipulate science, undermining PMI’s proclaimed transformation. Tobacco industry scientific practices remain a threat to public health, highlighting the urgent need for reform to protect science from the tobacco industry’s vested interests.

Implications
Japan is a key market for PMI, being a launch market for IQOS and having the highest heated tobacco product use globally. Our findings, in conjunction with other recent evidence, challenge PMI’s assertion that it is a source of credible science and cast doubt on the quality and ethical defensibility of its research, especially its studies conducted in Japan. This, in turn, brings into question the true public health impacts of its products. There is an urgent need to reform the way tobacco-related science is funded and conducted. Implementation of models through which research can be funded using the industry’s profits while minimizing its influence should be explored.
The nature and magnitude of cognitive impairment in narcolepsy type 1, narcolepsy type 2, and idiopathic hypersomnia: a meta-analysis
Authors: Harel Brian T , Gattuso James J , Latzman Robert D , Maruff Paul , Scammell Thomas E , Plazzi Giuseppe 
Published: June 2024

Abstract
People with narcolepsy type 1 (NT1), narcolepsy type 2 (NT2), and idiopathic hypersomnia (IH) often report cognitive impairment which can be quite burdensome but is rarely evaluated in routine clinical practice. In this systematic review and meta-analysis, we assessed the nature and magnitude of cognitive impairment in NT1, NT2, and IH in studies conducted from January 2000 to October 2022. We classified cognitive tests assessing memory, executive function, and attention by cognitive domain. Between-group differences were analyzed as standardized mean differences (Cohen’s d), and Cohen’s d for individual tests were integrated according to cognitive domain and clinical disease group. Eighty-seven studies were screened for inclusion; 39 satisfied inclusion criteria, yielding 73 comparisons (k): NT1, k = 60; NT2, k = 8; IH, k = 5. Attention showed large impairment in people with NT1 (d = −0.90) and IH (d = −0.97), and moderate impairment in NT2 (d = −0.60). Executive function was moderately impaired in NT1 (d = −0.30) and NT2 (d = −0.38), and memory showed small impairments in NT1 (d = −0.33). A secondary meta-analysis identified sustained attention as the most impaired domain in NT1, NT2, and IH (d ≈ −0.5 to −1). These meta-analyses confirm that cognitive impairments are present in NT1, NT2, and IH, and provide quantitative confirmation of reports of cognitive difficulties made by patients and clinicians. These findings provide a basis for the future design of studies to determine whether cognitive impairments can improve with pharmacologic and nonpharmacologic treatments for narcolepsy and IH.