bluuebunny/crossref_metadata_2025_split huggingface dataset:
Representing narrative evidence as clinical evidence logic statements
Authors: Lacson Ronilda , Eskian Mahsa , Cochon Laila , Gujrathi Isha , Licaros Andro , Zhao Anna , Vetrano Nicole , Schneider Louise , Raja Ali , Khorasani Ramin 
Published: April 2022

Abstract

Objective
Clinical evidence logic statements (CELS) are shareable knowledge artifacts in a semistructured “If-Then” format that can be used for clinical decision support systems. This project aimed to assess factors facilitating CELS representation.

Materials and Methods
We described CELS representation of clinical evidence. We assessed factors that facilitate representation, including authoring instruction, evidence structure, and educational level of CELS authors. Five researchers were tasked with representing CELS from published evidence. Represented CELS were compared with the formal representation. After an authoring instruction intervention, the same researchers were asked to represent the same CELS and accuracy was compared with that preintervention using McNemar’s test. Moreover, CELS representation accuracy was compared between evidence that is structured versus semistructured, and between CELS authored by specialty-trained versus nonspecialty-trained researchers, using χ2 analysis.

Results
261 CELS were represented from 10 different pieces of published evidence by the researchers pre- and postintervention. CELS representation accuracy significantly increased post-intervention, from 20/261 (8%) to 63/261 (24%, P value &lt; .00001). More CELS were assigned for representation with 379 total CELS subsequently included in the analysis (278 structured and 101 semistructured) postintervention. Representing CELS from structured evidence was associated with significantly higher CELS representation accuracy (P = .002), as well as CELS representation by specialty-trained authors (P = .0004).

Discussion
CELS represented from structured evidence had a higher representation accuracy compared with semistructured evidence. Similarly, specialty-trained authors had higher accuracy when representing structured evidence.

Conclusion
Authoring instructions significantly improved CELS representation with a 3-fold increase in accuracy. However, CELS representation remains a challenging task.
Contribution of the anaerobic blood culture vial for the recovery of Candida glabrata: A retrospective multicentric study
Authors: Farfour Eric , Le Brun Cecile , Mizrahi Assaf , Bargain Pauline , Durieux Marie-Fleur , Boquel Frédérique , Corvec Stéphane , Jeddi Fakhri , Muggeo Anaëlle , Huguenin Antoine , Barraud Olivier , Amara Marlène , Fihman Vincent , Bailly Eric , Botterel Françoise , Guillard Thomas , Vasse Marc ,   GMC study group, Guillouzouic Aurélie , d'Epenoux Louise Ruffier , Bémer Pascale , Juvin Marie-Emmanuelle , Woerther Paul-Louis , Foulet Francoise , Ammar Nawel Ait , Le Pape Patrice , Villena Isabelle , Des Champs Christophe , Mereghetti Laurent , Desoubeaux Guillaume , Le Monnier Alban , Ajzenberg Daniel , Maneglier Benjamin 
Published: April 2022

Abstract

Although Candida spp are aerobic microorganisms, some Candida strains, mainly Candida glabrata, can be recovered from anaerobic blood culture vials. We assessed the contribution of the anaerobic vials for the diagnosis of candidemia, especially for C. glabrata. We conducted a multicenter retrospective study including eight university or regional hospitals. A single episode of monomicrobial candidemia per patient was included from September 1st, 2016, to August 31st, 2019. The characteristics of all aerobic and anaerobic blood culture vials sampled within 2 h before and after the first positive blood culture vials were recorded (type of vials, result, and for positive vials time-to-positivity and Candida species). Overall, 509 episodes of candidemia were included. The main species were C. albicans (55.6%) followed by C. glabrata (17.1%), C. parapsilosis (4.9%), and C. tropicalis (4.5%). An anaerobic vial was positive in 76 (14.9%) of all episodes of which 56 (73.8%) were due to C. glabrata. The number of C. glabrata infections only positive in anaerobic vials was 1 (2.6%), 1 (11.1%), and 15 (37.5%) with the BACT/ALERT 3D the BACT/ALERT VIRTUO and the BACTEC FX instrument, respectively (P &lt; 0.01). The initial positivity of an anaerobic vial was highly predictive of the isolation of C. glabrata with the BACTEC FX (sensitivity of 96.8%). C. glabrata time-to-positivity was shorter in anaerobic vial than aerobic vial with all instruments. Anaerobic blood culture vials improve the recovery of Candida spp mainly C. glabrata. This study could be completed by further analyses including mycological and pediatric vials.

Lay summary
Although Candida spp are aerobic microorganisms, C. glabrata is able to grow in anaerobic conditions. In blood culture, the time-to-positivity of C. glabrata is shorter in anaerobic than aerobic vials. Only the anaerobic vial was positive in up to 15 (37.5%) C. glabrata bloodstream infections.
Chemical abundance of z ~ 6 quasar broad-line regions in the XQR-30 sample
Authors: Lai Samuel , Bian Fuyan , Onken Christopher A , Wolf Christian , Mazzucchelli Chiara , Bañados Eduardo , Bischetti Manuela , Bosman Sarah E I , Becker George , Cupani Guido , D’Odorico Valentina , Eilers Anna-Christina , Fan Xiaohui , Farina Emanuele Paolo , Onoue Masafusa , Schindler Jan-Torge , Walter Fabian , Wang Feige , Yang Jinyi , Zhu Yongda 
Published: April 2022

ABSTRACT
The elemental abundances in the broad-line regions of high-redshift quasars trace the chemical evolution in the nuclear regions of massive galaxies in the early Universe. In this work, we study metallicity-sensitive broad emission-line flux ratios in rest-frame UV spectra of 25 high-redshift (5.8 &lt; z &lt; 7.5) quasars observed with the VLT/X-shooter and Gemini/GNIRS instruments, ranging over $\log \left({{M}_{\rm {BH}}/\rm {M}_{\odot }}\right) = 8.4-9.8$ in black hole mass and $\log \left(\rm {L}_{\rm {bol}}/\rm {erg \, s}^{-1}\right) = 46.7-47.7$ in bolometric luminosity. We fit individual spectra and composites generated by binning across quasar properties: bolometric luminosity, black hole mass, and blueshift of the C iv line, finding no redshift evolution in the emission-line ratios by comparing our high-redshift quasars to lower redshift (2.0 &lt; z &lt; 5.0) results presented in the literature. Using cloudy-based locally optimally emitting cloud photoionization model relations between metallicity and emission-line flux ratios, we find the observable properties of the broad emission lines to be consistent with emission from gas clouds with metallicity that are at least 2–4 times solar. Our high-redshift measurements also confirm that the blueshift of the C iv emission line is correlated with its equivalent width, which influences line ratios normalized against C iv. When accounting for the C iv blueshift, we find that the rest-frame UV emission-line flux ratios do not correlate appreciably with the black hole mass or bolometric luminosity.
Preparing for low surface brightness science with the Vera C. Rubin Observatory: Characterization of tidal features from mock images
Authors: Martin G , Bazkiaei A E , Spavone M , Iodice E , Mihos J C , Montes M , Benavides J A , Brough S , Carlin J L , Collins C A , Duc P A , Gómez F A , Galaz G , Hernández-Toledo H M , Jackson R A , Kaviraj S , Knapen J H , Martínez-Lombilla C , McGee S , O’Ryan D , Prole D J , Rich R M , Román J , Shah E A , Starkenburg T K , Watkins A E , Zaritsky D , Pichon C , Armus L , Bianconi M , Buitrago F , Busá I , Davis F , Demarco R , Desmons A , García P , Graham A W , Holwerda B , Hon D S -H , Khalid A , Klehammer J , Klutse D Y , Lazar I , Nair P , Noakes-Kettel E A , Rutkowski M , Saha K , Sahu N , Sola E , Vázquez-Mata J A , Vera-Casanova A , Yoon I 
Published: April 2022

ABSTRACTTidal features in the outskirts of galaxies yield unique information about their past interactions and are a key prediction of the hierarchical structure formation paradigm. The Vera C. Rubin Observatory is poised to deliver deep observations for potentially millions of objects with visible tidal features, but the inference of galaxy interaction histories from such features is not straightforward. Utilizing automated techniques and human visual classification in conjunction with realistic mock images produced using the NewHorizon cosmological simulation, we investigate the nature, frequency, and visibility of tidal features and debris across a range of environments and stellar masses. In our simulated sample, around 80 per cent of the flux in the tidal features around Milky Way or greater mass galaxies is detected at the 10-yr depth of the Legacy Survey of Space and Time (30–31 mag arcsec−2), falling to 60 per cent assuming a shallower final depth of 29.5 mag arcsec−2. The fraction of total flux found in tidal features increases towards higher masses, rising to 10 per cent for the most massive objects in our sample (M⋆ ∼ 1011.5 M⊙). When observed at sufficient depth, such objects frequently exhibit many distinct tidal features with complex shapes. The interpretation and characterization of such features varies significantly with image depth and object orientation, introducing significant biases in their classification. Assuming the data reduction pipeline is properly optimized, we expect the Rubin Observatory to be capable of recovering much of the flux found in the outskirts of Milky Way mass galaxies, even at intermediate redshifts (z &lt; 0.2).
Shocked jets in CCSNe can power the zoo of fast blue optical transients
Authors: Gottlieb Ore , Tchekhovskoy Alexander , Margutti Raffaella 
Published: April 2022

ABSTRACTEvidence is mounting that recent multiwavelength detections of fast blue optical transients (FBOTs) in star-forming galaxies comprise a new class of transients, whose origin is yet to be understood. We show that hydrogen-rich collapsing stars that launch relativistic jets near the central engine can naturally explain the entire set of FBOT observables. The jet–star interaction forms a mildly relativistic shocked jet (inner cocoon) component, which powers cooling emission that dominates the high velocity optical signal during the first few weeks, with a typical energy of ∼1050–1051 erg. During this time, the cocoon radial energy distribution implies that the optical light curve exhibits a fast decay of $L \,\, \buildrel\propto \over \sim \,\,t^{-2.4}$. After a few weeks, when the velocity of the emitting shell is ∼0.01 c, the cocoon becomes transparent, and the cooling envelope governs the emission. The interaction between the cocoon and the dense circumstellar winds generates synchrotron self-absorbed emission in the radio bands, featuring a steady rise on a month time-scale. After a few months the relativistic outflow decelerates, enters the observer’s line of sight, and powers the peak of the radio light curve, which rapidly decays thereafter. The jet (and the inner cocoon) becomes optically thin to X-rays ∼day after the collapse, allowing X-ray photons to diffuse from the central engine that launched the jet to the observer. Cocoon cooling emission is expected at higher volumetric rates than gamma-ray bursts (GRBs) by a factor of a few, similar to FBOTs. We rule out uncollimated outflows, however, both GRB jets and failed collimated jets are compatible with all observables.
Implications of a net-zero target for India’s sectoral energy transitions and climate policy
Authors: Chaturvedi Vaibhav , Malyan Ankur 
Published: April 2022

Abstract
The IPCC 1.5°C report highlights the criticality of achieving a net-zero (NZ) greenhouse gas future. Many countries have announced their commitments to achieve a NZ future for their economies. India, while doing much more than its ‘fair share’ of mitigation, has yet to announce a NZ year target, presumably owing to the absence of an India-focused analysis on this issue. This study attempts to address this gap by modelling alternative peaking and NZ-year scenarios for India, and highlighting its implications for transition in energy-intensive sectors. We model four combinations of peaking and NZ-year scenarios for India (2030–50, 2030–60, 2040–70, and 2050–80) and a combination of technology availability scenarios related to carbon capture and storage and hydrogen within each of the policy scenarios. We present the implications of these 16 alternative scenarios for the required sectoral transitions across the electricity, transport, building and industrial sectors in India and provide insights for India’s climate policy.
PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave
Authors: Thieffry Axel , López-Márquez Diego , Bornholdt Jette , Malekroudi Mojgan Gholami , Bressendorff Simon , Barghetti Andrea , Sandelin Albin , Brodersen Peter 
Published: April 2022

Abstract
Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers and stabilizers of the growth-to-defense genetic reprogramming remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression. We show that around 15% of all transcription start sites (TSSs) rapidly induced during PTI define alternative transcription initiation events. From these, we identify clear examples of regulatory TSS change via alternative inclusion of target peptides or domains in encoded proteins, or of upstream open reading frames in mRNA leader sequences. We also find that 60% of PAMP response genes respond earlier than previously thought. In particular, a cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors (TFs) whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, examples of known potentiators of PTI, in one case under direct mitogen-activated protein kinase control, support the notion that the rapidly induced TFs could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state.
Fibrillin2 in chloroplast plastoglobules participates in photoprotection and jasmonate-induced senescence
Authors: Kim Inyoung , Kim Eun-Ha , Choi Yu-ri , Kim Hyun Uk 
Published: April 2022

Abstract
Fibrillins (FBNs) are the major structural proteins of plastoglobules (PGs) in chloroplasts. PGs are associated with defense against abiotic and biotic stresses, as well as lipid storage. Although FBN2 is abundant in PGs, its independent function under abiotic stress has not yet been identified. In this study, the targeting of FBN2 to PGs was clearly demonstrated using an FBN2-YFP fusion protein. FBN2 showed higher expression in green photosynthetic tissues and was upregulated at the transcriptional level under high-light stress. The photosynthetic capacity of fbn2 knockout mutants generated using CRISPR/Cas9 technology decreased rapidly compared with that of wild-type (WT) plants under high-light stress. In addition to the photoprotective function of FBN2, fbn2 mutants had lower levels of plastoquinone-9 and plastochromanol-8. The fbn2 mutants were highly sensitive to methyl jasmonate (MeJA) and exhibited root growth inhibition and a pale-green phenotype due to reduced chlorophyll content. Consistently, upon MeJA treatment, the fbn2 mutants showed faster leaf senescence and more rapid chlorophyll degradation with decreased photosynthetic ability compared with the WT plants. The results of this study suggest that FBN2 is involved in protection against high-light stress and acts as an inhibitor of jasmonate-induced senescence in Arabidopsis (Arabidopsis thaliana).
Examining the Relationship Between Reactive Stepping Outcomes and Falls in People With Multiple Sclerosis
Authors: Monaghan Andrew S , Mansfield Avril , Huisinga Jessie M , Peterson Daniel S 
Published: April 2022

Abstract

Objective
Reactive stepping is critical for preventing falls and is impaired in people with multiple sclerosis (PwMS); however, which aspects of stepping relate to falls remains poorly understood. Identifying outcomes most related to falls is a first step toward improving rehabilitation for fall prevention. The purpose of this study was to assess whether reactive step latency or length during forward and backward losses of balance were related to a history of falls in PwMS.

Methods
Of the 111 PwMS who participated in this study, 76 reported no falls in the previous 6 months, whereas 36 reported 1 or more falls. Participants completed 3 forward and 3 backward treadmill-induced reactive steps from stance. Step length (centimeters) and step latency (milliseconds) were measured using motion capture and analyzed via MATLAB.

Results
Participants with a history of falls had significantly slower step latencies during backward stepping, but not forward stepping, than those without a history of falls. Step length did not differ between groups. Slower step latencies during backward stepping significantly increased the odds of having experienced a fall (β = .908, SE = 0.403, odds ratio = 2.479, 95% CI = 1.125 to 5.464).

Conclusion
PwMS and a history of falling show delayed step onsets during backward reactive stepping. Specifically, for every 10-millisecond increase in step latency, PwMS were 2.5 times more likely to have a fall history. Although clinical trials are necessary to determine whether interventions targeting reactive stepping reduce falls in PwMS, the current work indicates that the latency of steps may be a relevant target for this work.

Impact
Subsequent fall prevention clinical trials should consider targeting backward reactive step latency to further assess its relevance for rehabilitation in PwMS.

Lay Summary
If you have MS and a history of falls, you may be more likely to have delayed reactive step latencies.
Application of osteoinductive calcium phosphate ceramics in giant cell tumor of the sacrum: report of six cases
Authors: Wang Yitian , Li Xiangfeng , Luo Yi , Zhang Li , Chen Hezhong , Min Li , Chang Qing , Zhou Yong , Tu Chongqi , Zhu Xiangdong , Zhang Xingdong 
Published: April 2022

AbstractThis study aimed at evaluating the possibility and effectiveness of osteoinductive bioceramics to fill the tumor cavity following the curettage of sacral giant cell tumor (GCT). Six patients (four females and two males, 25–45 years old) underwent nerve-sparing surgery, in which the tumor was treated by denosumab, preoperative arterial embolization and extensive curettage. The remaining cavity was filled with commercial osteoinductive calcium phosphate (CaP) bioceramics, whose excellent osteoinductivity was confirmed by intramuscular implantation in beagle canine. All patients were followed by computed tomography (CT) scans postoperatively. According to the modified Neer criterion, five cases obtained Type I healing status, and one case had Type II. At the latest follow-up, no graft-related complications and local recurrence were found. The CT scan indicated a median time of healing initiation of 3 months postoperatively, and the median time for relatively complete healing was 12 months. The excellent bone regenerative ability of the ceramics was also confirmed by increased CT attenuation value, blurred boundary and cortical rim rebuilding. In conclusion, osteoinductive CaP bioceramics could be an ideal biomaterial to treat the large remaining cavity following extensive curettage of sacral GCT. However, further investigation with more cases and longer follow-up was required to confirm the final clinical effect.
Corrigendum to: Addressing tobacco smoking and drinking to improve TB treatment outcomes, in South Africa: a feasibility study of the ProLife program
Authors: Louwagie Goedele M , Morojele Neo , Siddiqi Kamran , Mdege Noreen D , Tumbo John , Omole Olu , Pitso Lerato , Bachmann Max O , Ayo-Yusuf Olalekan A 
Published: April 2022

Abstract
Alcohol and tobacco use may lead to negative treatment outcomes in tuberculosis (TB) patients, and even more so if they are HIV-infected. We developed and tested the feasibility of a complex behavioral intervention (ProLife) delivered by lay health workers (LHWs) to improve treatment outcomes in TB patients who smoke tobacco and/or drink alcohol, at nine clinics in South Africa. The intervention comprised three brief motivational interviewing (MI) sessions augmented with a short message service (SMS) program, targeting as appropriate: tobacco smoking, harmful or hazardous drinking and medication adherence. Patients received SMSs twice a week. We measured recruitment and retention rates and assessed fidelity to the MI technique (MI Treatment Integrity 4.1 tool). Finally, we explored LHWs’ and patients’ experiences through interviews and semistructured questionnaires, respectively. We screened 137 TB patients and identified 14 smokers, 13 alcohol drinkers, and 18 patients with both behaviors. Participants’ mean age was 39.8 years, and 82.2% were men. The fidelity assessments pointed to the LHWs’ successful application of key MI skills, but failure to reach MI competency thresholds. Nevertheless, most patients rated the MI sessions as helpful, ascribed positive attributes to their counselors, and reported behavioral changes. SMSs were perceived as reinforcing but difficult language and technical delivery problems were identified as problems. The LHWs’ interview responses suggested that they (a) grasped the basic MI spirit but failed to understand specific MI techniques due to insufficient training practice; (b) perceived ProLife as having benefitted the patients (as well as themselves); (c) viewed the SMSs favorably; but (d) considered limited space and privacy at the clinics as key challenges. The ProLife program targeting multiple risk behaviors in TB patients is acceptable but LHW training protocol, and changes in wording and delivery of SMS are necessary to improve the intervention.
Trial registration: ISRCTN14213432
Decorin Inhibits Dermal Mesenchymal Cell Migration and Induces Scar Formation
Authors: Takaya Kento , Aramaki-Hattori Noriko , Sakai Shigeki , Okabe Keisuke , Asou Toru , Kishi Kazuo 
Published: April 2022

Background:
Variations in skin healing capacities are observed during different murine embryonic developmental stages. Through embryonic day 16 (E16), embryos are able to regenerate dermal architecture following flank skin wounding; however, after E17, wounds heal incompletely, inducing scar formation. The regenerative ability of the E16 fetal dermis depends on the migration of dermal mesenchymal cells. Decorin is a small molecule known to affect tissue tensile strength, cell phenotype, and tissue repair, including skin wound healing. In the current study, we evaluated the expression and roles of decorin in wound healing.

Methods:
Surgical injury was induced at E16 and E17 in ICR mouse embryos. Decorin expression was evaluated in tissue samples from these embryos using immunohistochemistry and reverse transcription quantitative polymerase chain reaction. Cell migration assays were used to evaluate wound healing capability of separated dermal and fascial tissues.

Results:
Our results showed that decorin exhibited distinct expression patterns during wound healing at E16 versus E17. Additionally, decorin expression altered cell migration in vitro. Dermal and fascial mesenchymal cells were found to exhibit distinct migration patterns concomitant with altered decorin expression. Specifically, decorin inhibited migration and favored scar formation.

Conclusion:
Decorin expression may contribute to scar formation in the late stage of mouse embryos by inhibiting the migration of dermal mesenchymal cells.