bluuebunny/crossref_metadata_2025_split huggingface dataset:
Re-evaluating the merits of decentralization as a core strategy for effective delivery of drug-resistant tuberculosis care in Pakistan
Authors: Khan Uzma , Lotia-Farrukh Ismat , Akhtar Ahwaz , Khowaja Saira N , Khan Salman , Madhani Falak , Parekh Asra , Adnan Sana , Ahmed Saman , Chaudhry Mariam , Hussain Hamidah , Habib Ali , Butt Shahid , Siddiqui Muhammad R , Ijaz Raafia , Jamal Saba , Khan Abdul B , Keshavjee Salmaan , Khan Aamir J , Salahuddin Naseem , Khan Palwasha Y 
Published: May 2022

Abstract
Decentralized, person-centred models of care delivery for drug-resistant tuberculosis (DR-TB) continue to be under-resourced in high-burden TB countries. The implementation of such models—made increasingly urgent by the COVID-19 pandemic—are key to addressing gaps in DR-TB care. We abstracted data of rifampicin-resistant (RR)/multidrug-resistant tuberculosis (MDR-TB) patients initiated on treatment at 11 facilities between 2010 and 2017 in Sindh and Balochistan provinces of Pakistan. We analysed trends in treatment outcomes relating to programme expansion to peri-urban and rural areas and estimated driving distance from patient residence to treatment facility. Among the 5586 RR/MDR-TB patients in the analysis, overall treatment success decreased from 82% to 66% between 2010 and 2017, as the programme expanded. The adjusted risk ratio for unfavourable outcomes was 1.013 (95% confidence interval 1.005–1.021) for every 20 km of driving distance. Our analysis suggests that expanding DR-TB care to centralized hubs added to increased unfavourable outcomes for people accessing care in peri-urban and rural districts. We propose that as enrolments increase, expanding DR-TB services close to or within affected communities is essential.
Temporal Patterns of Honeybee Foraging in a Diverse Floral Landscape Revealed Using Pollen DNA Metabarcoding of Honey
Authors: Jones Laura , Lowe Abigail , Ford Col R , Christie Lynda , Creer Simon , de Vere Natasha 
Published: May 2022

Synopsis
Understanding the plants pollinators use through the year is vital to support pollinator populations and mitigate for declines in floral resources due to habitat loss. DNA metabarcoding allows the temporal picture of nectar and pollen foraging to be examined in detail. Here, we use DNA metabarcoding to examine the forage use of honeybees (Apis mellifera L.) within a florally diverse landscape within the UK, documenting the key forage plants used and seasonal progression over two years. The total number of plant taxa detected in the honey was 120, but only 16 of these were found with a high relative read abundance of DNA, across the main foraging months (April–September). Only a small proportion of the available flowering genera in the landscape were used by the honeybees. The greatest relative read abundance came from native or near-native plants, including Rubus spp., Trifolium repens, the Maleae tribe including Crataegus, Malus, and Cotoneaster, and Hedera helix. Tree species were important forage in the spring months, followed by increased use of herbs and shrubs later in the foraging season. Garden habitat increased the taxon richness of native, near-native and horticultural plants found in the honey. Although horticultural plants were rarely found abundantly within the honey samples, they may be important for increasing nutritional diversity of the pollen forage.
Tamely Ramified Morphisms of Curves and Belyi’s Theorem in Positive Characteristic
Authors: Kedlaya Kiran S , Litt Daniel , Witaszek Jakub 
Published: May 2022

AbstractWe show that every smooth projective curve over a finite field $k$ admits a finite tame morphism to the projective line over $k$. Furthermore, we construct a curve with no such map when $k$ is an infinite perfect field of characteristic two. Our work leads to a refinement of the tame Belyi theorem in positive characteristic, building on results of Saïdi, Sugiyama–Yasuda, and Anbar–Tutdere.
Nipple Adenoma: Correlation of Imaging Findings and Histopathology
Authors: Leo Madeline E , Carter Gloria J , Waheed Uzma , Berg Wendie A 
Published: May 2022

Abstract
Nipple adenomas (NAs) are benign neoplasms composed of papillary hyperplasia of the epithelium of the major lactiferous ducts. Patients with NA may report bloody nipple discharge and clinically may resemble Paget disease, raising concern for malignancy. Mammographically, NAs are often occult. US can show a hypervascular circumscribed mass centered within the nipple with varying echogenicity. Diagnosis is usually made on punch biopsy or excision, but breast radiologists should be aware of this entity. Malignancy can be found elsewhere in the ipsilateral or contralateral breast, or very rarely may directly extend to involve an NA, but published experience with concurrent malignancies is small. We describe the radiologic-pathologic correlation of NAs.
Bleeding Complications After Breast Core-needle Biopsy—An Approach to Managing Patients on Antithrombotic Therapy
Authors: Goudreau Sally , Grimm Lars J , Srinivasan Ashmitha , Net Jose , Yang Roger , Dialani Vandana , Dodelzon Katerina 
Published: May 2022

Abstract
Image-guided core-needle breast and axillary biopsy (CNB) is the standard-of-care procedure for the diagnosis of breast cancer. Although the risks of CNB are low, the most common complications include bleeding and hematoma formation. Post-procedural bleeding is of particular concern in patients taking antithrombotic therapy, but there is currently no widely established standard protocol in the United States to guide antithrombotic therapy management. In the face of an increasing number of patients taking antithrombotic therapy and with the advent of novel classes of anticoagulants, the American College of Radiology guidelines recommend that radiologists consider cessation of antithrombotic therapy prior to CNB on a case-by-case basis. Lack of consensus results in disparate approaches to patients on antithrombotic therapy undergoing CNB. There is further heterogeneity in recommendations for cessation of antithrombotic therapy based on the modality used for image-guided biopsy, target location, number of simultaneous biopsies, and type of antithrombotic agent. A review of the available data demonstrates the safety of continuing antithrombotic therapy during CNB while highlighting additional procedural and target lesion factors that may increase the risk of bleeding. Risk stratification of patients undergoing breast interventional procedures is proposed to guide both pre-procedural decision-making and post-procedural management. Radiologists should be aware of antithrombotic agent pharmacokinetics and strategies to minimize post-procedural bleeding to safely manage patients.
Screening MRI in Women at Intermediate Breast Cancer Risk: An Update of the Recent Literature
Authors: Bahl Manisha 
Published: May 2022

Abstract
Guidelines issued by the American Cancer Society (ACS) in 2007 recommend neither for nor against screening MRI in women at intermediate breast cancer risk (15%–20%), including those with dense breast tissue, a history of lobular neoplasia or atypical ductal hyperplasia (ADH), or a prior breast cancer, because of scarce supporting evidence about the utility of MRI in these specific patient populations. However, since the issuance of the ACS guidelines in 2007, multiple investigations have found that women at intermediate risk may be suitable candidates for screening MRI, given the high detection rates of early-stage cancers and acceptable false-positive rates. For women with dense breast tissue, the Dense Tissue and Early Breast Neoplasm Screening trial reported that the incremental cancer detection rate (CDR) by MRI exceeded 16 cancers per 1000 examinations but decreased in the second round of screening; this decrease in CDR, however, occurred alongside a marked decrease in the false-positive rate. For women with lobular neoplasia or ADH, single-institution retrospective analyses have shown CDRs mostly ranging from 11 to 16 cancers per 1000 MRI examinations, with women with lobular carcinoma in situ benefitting more than women with atypical lobular hyperplasia or ADH. For patients with a prior breast cancer, the cancer yield by MRI varies widely but mostly ranges from 8 to 20 cancers per 1000 examinations, with certain subpopulations more likely to benefit, such as those with dense breasts. This article reviews and summarizes more recent studies on MRI screening of intermediate-risk women.
Deceiving Research Participants: Is It Inconsistent With Valid Consent?
Authors: Wendler David 
Published: May 2022

AbstractIt is widely assumed that the use of deception in research is always inconsistent with obtaining valid consent. In addition, guidelines and regulations permit research without valid consent only when it poses no greater than minimal risk. Current practice thus prohibits studies that use deception and pose greater than minimal risk, including studies that rely on deceptive methods to evaluate experimental treatments. To assess whether these prohibitions are justified, the present paper evaluates five arguments that might be thought to support the assumption that deception is always inconsistent with valid consent. Analysis of these arguments reveals that deception is frequently, but not always, inconsistent with obtaining valid consent for research. This conclusion suggests that, in order to avoid unnecessarily blocking valuable research, current policies and practice should be revised to recognize the conditions under which the use of deception can be consistent with obtaining research participants’ valid consent.
The impact of ultraviolet heating and cooling on the dynamics and observability of lava planet atmospheres
Authors: Nguyen T Giang , Cowan Nicolas B , Pierrehumbert Raymond T , Lupu Roxana E , Moores John E 
Published: May 2022

ABSTRACT
Lava planets have non-global, condensible atmospheres similar to icy bodies within the Solar system. Because they depend on interior dynamics, studying the atmospheres of lava planets can lead to understanding unique geological processes driven by their extreme environment. Models of lava planet atmospheres have thus far focused on either radiative transfer or hydrodynamics. In this study, we couple the two processes by introducing ultraviolet (UV) and infrared (IR) radiation to a turbulent boundary layer model. We also test the effect of different vertical temperature profiles on atmospheric dynamics. Results from the model show that UV radiation affects the atmosphere much more than IR. UV heating and cooling work together to produce a horizontally isothermal atmosphere away from the substellar point regardless of the vertical temperature profile. We also find that stronger temperature inversions induce stronger winds and hence cool the atmosphere. Our simulated transmission spectra of the bound atmosphere show a strong SiO feature in the UV that would be challenging to observe in the planet’s transit spectrum due to the precision required. Our simulated emission spectra are more promising, with significant SiO spectral features at 4.5 and 9 $\mu$m that can be observed with the James Webb Space Telescope. Different vertical temperature profiles produce discernible dayside emission spectra, but not in the way one would expect.
Investigating the nature and properties of MAXI J1810−222 with radio and X-ray observations
Authors: Russell T D , Del Santo M , Marino A , Segreto A , Motta S E , Bahramian A , Corbel S , D’Aì A , Salvo T Di , Miller-Jones J C A , Pinto C , Pintore F , Tzioumis A 
Published: May 2022

ABSTRACT
We present results from radio and X-ray observations of the X-ray transient MAXI J1810−222. The nature of the accretor in this source has not been identified. In this paper, we show results from a quasi-simultaneous radio and X-ray monitoring campaign taken with the Australia Telescope Compact Array, the Neil Gehrels Swift Observatory X-ray Telescope (XRT), and the Swift Burst Alert Telescope. We also analyse the X-ray temporal behaviour using observations from the Neutron star Interior Composition Explorer. Results show a seemingly peculiar X-ray spectral evolution of MAXI J1810−222 during this outburst, where the source was initially only detected in the soft X-ray band for the early part of the outburst. Then, ∼200 d after MAXI J1810−222 was first detected the hard X-ray emission increased and the source transitioned to a long-lived (∼1.5 yr) bright, harder X-ray state. After this hard state, MAXI J1810−222 returned back to a softer state, before fading and transitioning again to a harder state and then appearing to follow a more typical outburst decay. From the X-ray spectral and timing properties, and the source’s radio behaviour, we argue that the results from this study are most consistent with MAXI J1810−222 being a relatively distant (≳6 kpc) black hole X-ray binary. A sufficiently large distance to source can simply explain the seemingly odd outburst evolution that was observed, where only the brightest portion of the outburst was detectable by the all-sky XRTs.
Three-dimensional simulations of the jet feedback mechanism in common envelope jets supernovae
Authors: Hillel Shlomi , Schreier Ron , Soker Noam 
Published: May 2022

ABSTRACT
We conduct three-dimensional hydrodynamical simulations of common envelope jets supernova (CEJSN) events where we assume that a neutron star (NS) launches jets as it orbits inside the outer zones of a red supergiant (RSG) envelope, and find the negative jet feedback coefficient to be ≃ 0.1–0.2. This coefficient is the factor by which the jets reduce the mass accretion rate on to the NS as they remove mass from the envelope and inflate bubbles (cocoons). Our results suggest that in most CEJSN events the NS-RSG binary system experiences the grazing envelope evolution before it enters a full common envelope evolution (CEE). We also find that the jets induce upward and downward flows in the RSG envelope. These flows together with the strong convection of RSG stars might imply that energy transport by convection in CEJSNe is very important. Because of limited numerical resources we do not include in the simulations the gravity of the NS, nor the accretion process, nor the jets launching process, and nor the gravity of the deformed envelope. Future numerical simulations of CEE with a NS/BH companion should include the accretion process on to the NS (and vary the jets’ power accordingly), the full gravitational interaction of the NS with the RSG, and energy transport by the strong convection.
Parallel Evolution of Ameloblastic scpp Genes in Bony and Cartilaginous Vertebrates
Authors: Leurs Nicolas , Martinand-Mari Camille , Marcellini Sylvain , Debiais-Thibaud Mélanie 
Published: May 2022

Abstract
In bony vertebrates, skeletal mineralization relies on the secretory calcium-binding phosphoproteins (Scpp) family whose members are acidic extracellular proteins posttranslationally regulated by the Fam20°C kinase. As scpp genes are absent from the elephant shark genome, they are currently thought to be specific to bony fishes (osteichthyans). Here, we report a scpp gene present in elasmobranchs (sharks and rays) that evolved from local tandem duplication of sparc-L 5′ exons and show that both genes experienced recent gene conversion in sharks. The elasmobranch scpp is remarkably similar to the osteichthyan scpp members as they share syntenic and gene structure features, code for a conserved signal peptide, tyrosine-rich and aspartate/glutamate-rich regions, and harbor putative Fam20°C phosphorylation sites. In addition, the catshark scpp is coexpressed with sparc-L and fam20°C in tooth and scale ameloblasts, similarly to some osteichthyan scpp genes. Despite these strong similarities, molecular clock and phylogenetic data demonstrate that the elasmobranch scpp gene originated independently from the osteichthyan scpp gene family. Our study reveals convergent events at the sparc-L locus in the two sister clades of jawed vertebrates, leading to parallel diversification of the skeletal biomineralization toolkit. The molecular evolution of sparc-L and its coexpression with fam20°C in catshark ameloblasts provides a unifying genetic basis that suggests that all convergent scpp duplicates inherited similar features from their sparc-L precursor. This conclusion supports a single origin for the hypermineralized outer odontode layer as produced by an ancestral developmental process performed by Sparc-L, implying the homology of the enamel and enameloid tissues in all vertebrates.
GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA
Authors: Ghani Nur Syatila Ab , Emrizal Reeki , Moffit Sabrina Mohamed , Hamdani Hazrina Yusof , Ramlan Effirul Ikhwan , Firdaus-Raih Mohd 
Published: May 2022

Abstract
The GrAfSS (Graph theoretical Applications for Substructure Searching) webserver is a platform to search for three-dimensional substructures of: (i) amino acid side chains in protein structures; and (ii) base arrangements in RNA structures. The webserver interfaces the functions of five different graph theoretical algorithms – ASSAM, SPRITE, IMAAAGINE, NASSAM and COGNAC – into a single substructure searching suite. Users will be able to identify whether a three-dimensional (3D) arrangement of interest, such as a ligand binding site or 3D motif, observed in a protein or RNA structure can be found in other structures available in the Protein Data Bank (PDB). The webserver also allows users to determine whether a protein or RNA structure of interest contains substructural arrangements that are similar to known motifs or 3D arrangements. These capabilities allow for the functional annotation of new structures that were either experimentally determined or computationally generated (such as the coordinates generated by AlphaFold2) and can provide further insights into the diversity or conservation of functional mechanisms of structures in the PDB. The computed substructural superpositions are visualized using integrated NGL viewers. The GrAfSS server is available at http://mfrlab.org/grafss/.
Prevalence, Clinical Characteristics, and Outcomes of Sepsis Caused by Severe Acute Respiratory Syndrome Coronavirus 2 Versus Other Pathogens in Hospitalized Patients With COVID-19
Authors: Shappell Claire N. , Klompas Michael , Kanjilal Sanjat , Chan Christina , Rhee Chanu 
Published: May 2022

IMPORTANCE:
The prevalence and causes of sepsis in patients hospitalized with COVID-19 are poorly characterized.

OBJECTIVES:
To investigate the prevalence, clinical characteristics, and outcomes of sepsis caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) versus other pathogens in patients hospitalized with COVID-19.

DESIGN, SETTING, AND PARTICIPANTS:
Cross-sectional, retrospective chart review of 200 randomly selected patients hospitalized with COVID-19 at four Massachusetts hospitals between March 2020 and March 2021.

MAIN OUTCOMES AND MEASURES:
The presence or absence of sepsis was determined per Sepsis-3 criteria (infection leading to an increase in Sequential Organ Failure Assessment score by ≥ 2 points above baseline). Sepsis episodes were assessed as caused by SARS-CoV-2, other pathogens, or both. Rates of organ dysfunction and in-hospital death were also assessed.

RESULTS:
Sepsis was present in 65 of 200 COVID-19 hospitalizations (32.5%), of which 46 of 65 sepsis episodes (70.8%) were due to SARS-CoV-2 alone, 17 of 65 (26.2%) were due to both SARS-CoV-2 and non-SARS-CoV-2 infections, and two of 65 (3.1%) were due to bacterial infection alone. SARS-CoV-2–related organ dysfunction in patients with sepsis occurred a median of 1 day after admission (interquartile range, 0–2 d) and most often presented as respiratory (93.7%), neurologic (46.0%), and/or renal (39.7%) dysfunctions. In-hospital death occurred in 28 of 200 COVID-19 hospitalizations (14.0%), including two of 135 patients without sepsis (1.5%), 16 of 46 patients with sepsis (34.8%) due to SARS-CoV-2 alone, and 10 of 17 patients with sepsis (58.8%) due to both SARS-CoV-2 and bacterial pathogens.

CONCLUSIONS:
Sepsis occurred in one in three patients hospitalized with COVID-19 and was primarily caused by SARS-CoV-2 itself, although bacterial infection also contributed in a quarter of sepsis cases. Mortality in COVID-19 patients with sepsis was high, especially in patients with mixed SARS-CoV-2 and bacterial sepsis. These findings affirm SARS-CoV-2 as an important cause of sepsis and highlight the need to improve surveillance, recognition, prevention, and treatment of both viral and bacterial sepsis in hospitalized patients with COVID-19.
Cloud adoption in Indian SMEs – an empirical analysis
Authors: Shetty Jayalaxmi Padmanabha , Panda Rajesh 
Published: May 2022

PurposeThis study aims to empirically validate the determinants of cloud adoption in small and medium enterprises (SMEs) in India and examine its impact on their economic performance.Design/methodology/approachAn integrated theoretical model interplaying technological, organizational and environmental aspects were applied for analyzing the variation in factors. Using data from 317 Indian SMEs, we have applied confirmatory factor analysis and structural equation modeling to test the hypotheses.FindingsThe results demonstrated that perceived usefulness, perceived ease of use, technology readiness, top management support and trust were the influencing drivers of cloud adoption in SMEs in India. Compared to previous studies, we did not find compatibility and competitive pressure as significant, suggesting that there was no single set of factors influencing technology adoption. Economic performance achieved by reduced transaction costs formed the basis of favorable adoption.Research limitations/implicationsThe integrated model can provide space for new dimensions based on the category and geography of the SMEs. The paper does not address the supply-chain perspective of cloud adoption.Practical implicationsThe study directs the firm owners to visualize business logic by creating a digital ecosystem. Further, the model guides the stakeholders, including cloud service providers, to contribute to the economic proficiency of the SMEs.Originality/valueThe paper empirically validates a model integrating both the drivers and consequences of cloud computing adoption as a unique study. Findings indicate that the usage of metrics such as return on investment and system efficiency form a part of the technology system approach.