bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft genomes of 3 cyanobacteria strains and 17 co-habiting proteobacteria assembled from metagenomes
Authors: Berthold Maximilian , Albrecht Martin , Campbell Douglas A. , Omar Naaman M. 
Published: November 2023

ABSTRACT

Cyanobium
and
Synechococcus
are prominent, globally distributed cyanobacteria genera with ecological significance. Here, we report the genomes of the marine
Synechococcus
sp. CCMP836 and two strains of
Cyanobium
(CZS25K and CZS48M) along with the genomes of 17 co-occurring proteobacteria. These genomes will improve the strain-specific ecological positions.
Single Top Quark Production in $${s}$$ Channel at Ultra-High Energies
Authors: Okorokov V. A. 
Published: November 2023

Abstract
The processes with single top quark production provide a prototype search for the types of final state that are expected in many new physics scenarios. Some distinctive features are considered for particle production in the top sector in ultra-high energy domain which can be covered partly in the collisions of cosmic ray particles with atmosphere. The single top quark production through electroweak interaction is studied within the Standard Model and the Effective Field Theory approach used for calculations of total partonic cross sections in $$s$$–channel. These quantitative results can be important for both the future collider experiments at center-of-mass energy frontier and the improvement of the phenomenological models for development of the cosmic ray cascades in ultra-high energy domain. Thus the study allows the better understanding of heavy particle production and emphasizes the exciting interrelation between the high-energy physics on accelerators and ultra-high energy cosmic ray measurements.
Prevalence of bradycardia in 4876 newborns in the first minute after birth and association with positive pressure ventilation: a population-based cross-sectional study
Authors: Rettedal Siren , Kibsgaard Amalie , Kvaløy Jan Terje , Eilevstjønn Joar , Ersdal Hege Langli 
Published: November 2023

ObjectiveTo determine the prevalence of bradycardia in the first minute after birth and association with positive pressure ventilation (PPV).MethodA population-based cross-sectional study was conducted from June 2019 to December 2021 at Stavanger University Hospital, Norway. Parents consented to participation during pregnancy, and newborns ≥28 weeks’ gestation were included at birth. Heart rate (HR) was captured immediately after birth and continuously for the first minute(s). Time of birth was registered on a tablet. Provision of PPV was captured using video.ResultsOf 4876 included newborns, 164 (3.4%) did not breathe (two-thirds) or breathed ineffectively (one-third) and received PPV at birth. HR in the first minute had a wide distribution. The prevalence of first measured HR <100 and <60 beats/minute at median 16 s was 16.3% and 0.6%, respectively. HR increased in most cases. At 60 s, 3.7% had HR <100 beats/minute, of which 82% did not require PPV. In total, 25% of newborns had some registered HR <100 beats/minute during the first minute, of which 95% did not require PPV. Among newborns who received PPV, 76% and 62% had HR ≥100 beats/minute at 60 s and at start PPV, respectively.ConclusionBradycardia with HR <100 bpm in the first minute of life was frequent, but mostly self-resolved. Among the 4% of newborns that remained bradycardic at 60 s, only 20% received PPV. Two-thirds of resuscitated newborns had HR ≥100 beats/minute at start PPV. None of the ventilated newborns were breathing adequately at start PPV.Trial registration numberNCT03849781.
Prevalence of pre-existing lung diseases and their association with income level among patients with lung cancer: a nationwide population-based case-control study in South Korea
Authors: Oh Chang-Mo , Lee Sanghee , Kwon Hoejun , Hwangbo Bin , Cho Hyunsoon 
Published: November 2023

BackgroundThis study aimed to estimate the prevalence of pre-existing lung diseases in patients with lung cancer compared to people without lung cancer and examine the association between income levels and pre-existing lung diseases.MethodsData on patients with lung cancer (case) and the general population without lung cancer (non-cancer controls) matched by age, sex and region were obtained from the Korea National Health Insurance Service—National Health Information Database (n=51 586). Insurance premiums were divided into quintiles and medicaid patients. Conditional logistic regression models were used to examine the association between pre-existing lung diseases and the risk of lung cancer. The relationship between income level and the prevalence of pre-existing lung disease among patients with lung cancer was analysed using logistic regression models.ResultsThe prevalence of asthma (17.3%), chronic obstructive lung disease (COPD) (9.3%), pneumonia (9.1%) and pulmonary tuberculosis (1.6%) in patients with lung cancer were approximately 1.6–3.2 times higher compared with the general population without lung cancer. A significantly higher risk for lung cancer was observed in individuals with pre-existing lung diseases (asthma: OR=1.36, 95% CI 1.29 to 1.44; COPD: 2.11, 95% CI 1.94 to 2.31; pneumonia: 1.49, 95% CI 1.38 to 1.61; pulmonary tuberculosis: 2.16, 95% CI 1.75 to 2.66). Patients with lung cancer enrolled in medicaid exhibited higher odds of having pre-existing lung diseases compared with those in the top 20% income level (asthma: OR=1.75, 95% CI 1.56 to 1.96; COPD: 1.91, 95% CI 1.65 to 2.21; pneumonia: 1.73, 95% CI 1.50 to 2.01; pulmonary tuberculosis: 2.45, 95% CI 1.78 to 3.36).ConclusionsPre-existing lung diseases were substantially higher in patients with lung cancer than in the general population. The high prevalence odds of pre-existing lung diseases in medicaid patients suggests the health disparity arising from the lowest income group, underscoring a need for specialised lung cancer surveillance.
A clinical decision rule to rule out bloodstream infection in the emergency department: retrospective multicentric observational cohort study
Authors: Pehlivan Jonathan , Douillet Delphine , Jérémie Riou , Perraud Clément , Niset Alexandre , Eveillard Matthieu , Chenouard Rachel , Mahieu Rafael 
Published: November 2023

BackgroundWe aimed to identify patients at low risk of bloodstream infection (BSI) in the ED.MethodsWe derived and validated a prediction model to rule out BSI in the ED without the need for laboratory testing by determining variables associated with a positive blood culture (BC) and assigned points according to regression coefficients. This retrospective study included adult patients suspected of having BSI (defined by at least one BC collection) from two European ED between 1 January 2017 and 31 December 2019. The primary end point was the BSI rate in the validation cohort for patients with a negative Bacteremia Rule Out Criteria (BAROC) score. The effect of adding laboratory variables to the model was evaluated as a second step in a two-step diagnostic strategy.ResultsWe analysed 2580 patients with a mean age of 64 years±21, of whom 46.1% were women. The derived BAROC score comprises 12 categorical clinical variables. In the validation cohort, it safely ruled out BSI without BCs in 9% (58/648) of patients with a sensitivity of 100% (95% CI 95% to 100%), a specificity of 10% (95% CI 8% to 13%) and a negative predictive value of 100% (95% CI 94% to 100%). Adding laboratory variables (creatinine ≥177 µmol/L (2.0 mg/dL), platelet count ≤150 000/mm3and neutrophil count ≥12 000/mm3) to the model, ruled out BSI in 10.2% (58/570) of remaining patients who had been positive on the BAROC score. The BAROC score with laboratory results had a sensitivity of 100% (95% CI 94% to 100%), specificity of 11% (95% CI 9% to 14%) and negative predictive value of 100% (95% CI 94 to 100%). In the validation cohort, there was no evidence of a difference in discrimination between the area under the receiver operating characteristic for BAROC score with versus without laboratory testing (p=0.6).ConclusionThe BAROC score safely identified patients at low risk of BSI and may reduce BC collection in the ED without the need for laboratory testing.
Optimal carcinoembryonic antigen (CEA) cutoff values in the diagnosis of neoplastic mucinous pancreatic cysts differ among assays
Authors: Kim David , Margolskee Elizabeth , Goyal Abha , Siddiqui Momin T , Heymann Jonas J , Rao Rema , Hayden Joshua 
Published: November 2023

AimPancreatic cyst fluid carcinoembryonic antigen (CEA) is a pivotal test in the diagnosis and management of neoplastic mucinous cysts (NMC) of the pancreas. Cyst fluid CEA levels of 192 ng/mL have been widely used to identify NMC. However, CEA values are unique to and significantly differ between individual assays with various optimal cutoffs reported in the literature for NMC. Here, we investigate the optimal CEA cut-off value of pancreatic cysts from two different assays to identify differences in thresholds.MethodsPancreatic cyst fluid CEA levels, CEA assay platform (Beckman Dxl (BD) or Siemens Centaur XP (SC)), and clinical/pathological information were retrospectively collected. Cases were categorised into either NMC or non-NMC. Optimal CEA cut-off values were calculated via a receiver operator characteristic curve. Cut-off values were then identified separately by assay platform.ResultsIn total, 149 pancreatic cystic lesions with concurrent CEA values (SC: n=47; BD: n=102) were included. Histological correlation was available for 26 (17%) samples. The optimal CEA cut-off value for all samples at the study institution was 45.9 ng/mL (area under the curve (AUC)=86, Sn=85.7%, Sp=73.8%). When analysed separately by CEA assay, the cut-off values were 45.9 ng/mL (AUC=84.27, Sn=89.7%, Sp=71.4%) for BD and 24.4 ng/mL (AUC=77, Sn=81.8%, Sp=75%) for SC (p=0.48).ConclusionsThis study showed an optimal pancreas cyst CEA cut-off threshold of 45.9 ng/mL, which is lower than commonly cited literature with different cutoffs on the two separate platforms (BD: 45.9 ng/mL, SC: 24.4 ng/mL).
MACE and VTE across upadacitinib clinical trial programmes in rheumatoid arthritis, psoriatic arthritis and ankylosing spondylitis
Authors: Charles-Schoeman Christina , Choy Ernest , McInnes Iain B , Mysler Eduardo , Nash Peter , Yamaoka Kunihiro , Lippe Ralph , Khan Nasser , Shmagel Anna K , Palac Hannah , Suboticki Jessica , Curtis Jeffrey R 
Published: November 2023

ObjectivesTo provide an integrated analysis of major adverse cardiovascular events (MACEs) and events of venous thromboembolism (VTE) and associated risk factors across rheumatoid arthritis (RA), psoriatic arthritis (PsA), and ankylosing spondylitis (AS) phase 2b/3 upadacitinib clinical programmes.MethodsData were analysed and summarised from clinical trials of RA, PsA and AS treated with upadacitinib 15 mg once daily (QD) and 30 mg QD (as of 30 June 2021). Data from adalimumab (RA and PsA) and methotrexate (RA) arms were included as comparators. Adjudicated MACEs and VTE events were presented as exposure-adjusted rates per 100 patient-years (E/100 PY). Univariable Cox proportional hazard regression analyses assessed potential associations of risk factors for MACE and VTE.ResultsIn total, 4298 patients received upadacitinib 15 mg (RA n=3209, PsA n=907 and AS n=182) and 2125 patients received upadacitinib 30 mg (RA n=1204 and PsA n=921). In patients with RA and PsA, rates of MACE (0.3–0.6 E/100 PY) and VTE (0.2–0.4 E/100 PY) were similar across upadacitinib doses; in patients with AS, no MACEs and one VTE event occurred. Most patients experiencing MACEs or VTE events had two or more baseline cardiovascular risk factors. Across RA and PsA groups, rates of MACEs and VTE events were similar.ConclusionsRates of MACEs and VTE events with upadacitinib were consistent with previously reported data for patients receiving conventional synthetic and biologic disease-modifying anti-rheumatic drugs and comparable with active comparators adalimumab and methotrexate. Associated patient characteristics are known risk factors for MACEs and VTE events.Trial registration numbersRA (SELECT-NEXT:NCT02675426; SELECT-MONOTHERAPY:NCT02706951; SELECT-BEYOND:NCT02706847; SELECT-COMPARE:NCT02629159; SELECT-EARLY:NCT02706873, SELECT-CHOICE:NCT03086343), PsA (SELECT-PsA 2:NCT03104374; SELECT-PsA 1:NCT03104400), and AS (SELECT-AXIS 1:NCT03178487).
Antimicrobial susceptibility profile ofNeisseria gonorrhoeaefrom patients attending a medical laboratory, Institut Pasteur de Madagascar between 2014 and 2020: phenotypical and genomic characterisation in a subset ofNeisseria gonorrhoeaeisolates
Authors: Rafetrarivony Lala Fanomezantsoa , Rabenandrasana Mamitina Alain Noah , Hariniaina Elisoa Ratsima , Randrianirina Frédérique , Smith Anthony Marius , Crucitti Tania 
Published: November 2023

ObjectivesAntimicrobial-resistantNeisseria gonorrhoeae(NG) is a concern. Little is known about antimicrobial susceptibility profiles and associated genetic resistance mechanisms of NG in Madagascar. We report susceptibility data of NG isolates obtained by the medical laboratory (CBC) of the Institut Pasteur de Madagascar, Antananarivo, Madagascar, during 2014–2020. We present antimicrobial resistance mechanisms data and phenotype profiles of a subset of isolates.MethodsWe retrieved retrospective data (N=395) from patients with NG isolated during 2014−2020 by the CBC. We retested 46 viable isolates including 6 found ceftriaxone and 2 azithromycin resistant, as well as 33 isolated from 2020. We determined minimal inhibitory concentrations for ceftriaxone, ciprofloxacin, azithromycin, penicillin, tetracycline and spectinomycin using Etest. We obtained whole-genome sequences and identified the gene determinants associated with antimicrobial resistance and the sequence types (STs).ResultsOver the study period, ceftriaxone-resistant isolates exceeded the threshold of 5% in 2017 (7.4% (4 of 54)) and 2020 (7.1% (3 of 42)). All retested isolates were found susceptible to ceftriaxone, azithromycin and spectinomycin, and resistant to ciprofloxacin. The majority were resistant to penicillin (83% (38 of 46)) and tetracycline (87% (40 of 46)). We detected chromosomal mutations associated with antibiotic resistance ingyrA, parC, penA, ponA,porBandmtrRgenes. None of the retested isolates carried the mosaicpenAgene. The high rate of resistance to penicillin and tetracycline is explained by the presence ofblaTEM(94.7% (36 of 38)) andtetM(97.5% (39 of 40)). We found a high number of circulating multilocus STs. Almost half of them were new types, and one new type was among the four most predominant.ConclusionsOur report provides a detailed dataset obtained through phenotypical and genotypical methods which will serve as a baseline for future surveillance of NG. We could not confirm the occurrence of ceftriaxone-resistant isolates. Our results highlight the importance of implementing quality-assured gonococcal antimicrobial resistance surveillance in Madagascar.
Impact of intravenous administration of nalbuphine at different time points for postoperative analgesia and sedation in adenotonsillectomized children: a prospective, randomized controlled trial
Authors: Cao Hongmin , Bao Chunying , Tu Haiya , Gao Jing , Huang Jinjin , Chen Qixing 
Published: November 2023

ObjectiveTo compare the efficacy of intravenous administration of nalbuphine at different time points for postoperative analgesia and sedation in adenotonsillectomized children.MethodsPatients with obstructive sleep apnea syndrome scheduled for adenotonsillectomy were randomly divided into group A (patients received intravenous nalbuphine 0.2 mg/kg before anesthesia induction), group B (patients received intravenous nalbuphine 0.2 mg/kg 10 min before the end of surgery), and group C (patients did not receive nalbuphine injection). The time points for measuring outcomes were before anesthesia induction (T0), extubation (T1), and 0, 15, 30, or 45 min in the postanesthesia care unit (PACU) (T2–T5, respectively).ResultsThere were 40 patients in group A, 41 patients in group B and 39 patients in group C. Patients in group B had significantly lower FLACC (Face, Legs, Activity, Cry, Consolability) pain scores at T2–T5 than those in group C (all p<0.05). Patients in group B had higher Ramsay Sedation Score at T2–T4 than those in group C (all p<0.05). The proportion of patients who received remedial analgesia in the PACU in group A (17.5%, p=0.008) and group B (9.8%, p<0.001) was significantly lower than that in group C (46.2%).ConclusionIntravenous administration of nalbuphine 10 min before the end of adenotonsillectomy in children could decrease pain intensity and increase sedation levels during the recovery period with the reduction of remedial analgesia in the PACU.Trial registration numberChiCTR2200060118.
Acute oral antioxidant consumption does not alter brachial artery flow mediated dilation in young adults independent of exercise training status
Authors: King Trevor J. , Petrick Heather L. , Millar Philip J. , Burr Jamie F. 
Published: November 2023

Endothelium-dependent vasodilation can be tested using a variety of shear stress paradigms, some of which may involve the production of reactive oxygen species. The purpose of this study was to compare different methods for assessing endothelial function and their specific involvement of reactive oxygen species and influence of aerobic training status. Twenty-nine (10 F) young and healthy participants (VO2max: 34–74 mL·kg−1·min−1) consumed either an antioxidant cocktail (AOC; vitamin C, vitamin E, α-lipoic acid) or placebo (PLA) on each of two randomized visits. Endothelial function was measured via three different brachial artery flow-mediated dilation (FMD) tests: reactive hyperemia (RH-FMD: 5 min cuff occlusion and release), sustained shear (SS-FMD: 6 min rhythmic handgrip), and progressive sustained shear (P-SS-FMD: three intensities of 3 min of rhythmic handgrip). Baseline artery diameter decreased (all tests: 3.8 ± 0.5 to 3.7 ± 0.6 mm, p = 0.004), and shear rate stimulus increased (during RH-FMD test, p = 0.021; during SS-FMD test, p = 0.36; during P-SS-FMD test, p = 0.046) following antioxidant consumption. However, there was no difference in FMD following AOC consumption (RH-FMD, PLA: 8.1 ± 2.6%, AOC: 8.2 ± 3.5%, p = 0.92; SS-FMD, PLA: 6.9 ± 3.9%, AOC: 7.8 ± 5.2%, p = 0.15) or FMD per shear rate slope (P-SS-FMD: PLA: 0.0039 ± 0.0035 mm·s−1, AOC: 0.0032 ± 0.0017 mm·s−1, p = 0.28) and this was not influenced by training status/fitness (all p > 0.60). Allometric scaling did not alter these outcomes (all p > 0.40). Reactive oxygen species may not be integral to endothelium-dependent vasodilation tested using reactive, sustained, or progressive shear protocols in young males and females, regardless of fitness level.
How do different thinning methods influence spatial tree diversity in mixed forest stands of planted Norway spruce (Picea abies L.) and naturally regenerated birch (Betula spp.) in southern Sweden?
Authors: Becs Artis , Bergström Dan , Egnell Gustaf , Pommerening Arne 
Published: November 2023

Forest biomass has become a viable alternative energy source for replacing fossil fuels, particularly after the European Union acknowledged its sustainability status. To reach zero net greenhouse gas emissions by 2045 in Sweden, new efficient methods of biomass extraction, such as geometrical biomass thinnings, are being explored and tested. These machine-based methods involve the extraction of above-ground biomass in narrow, 1–2 m-wide strips between extraction racks. While evidence-based optimization of biomass extraction mostly focuses on time- and cost-efficiency and on stand growth, criteria such as tree diversity are often overlooked. However, with ongoing climate change, tree diversity is crucial to strengthening the resilience and productivity of future forests, which also enhance the provision of ecosystem services and overall biological diversity. Therefore, we studied the effects of different biomass thinning strategies on spatial tree diversity in southern Sweden using nearest-neighbour summary statistics. We found scientific evidence that different geometrical designs of biomass thinning, especially in 1 or 2 m-wide strips, resulted in higher spatial tree diversity compared to conventional biomass thinning. Hence, in mixed conifer-broadleaved forests, biomass thinning in 1 or 2 m-wide strips is recommended for maintaining spatial tree diversity.
Efficient Neural Ranking Using Forward Indexes and Lightweight Encoders
Authors: Leonhardt Jurek , Müller Henrik , Rudra Koustav , Khosla Megha , Anand Abhijit , Anand Avishek 
Published: November 2023

Dual-encoder-based dense retrieval models have become the standard in IR. They employ large Transformer-based language models, which are notoriously inefficient in terms of resources and latency.We proposeFast-Forwardindexes—vector forward indexes which exploit the semantic matching capabilities of dual-encoder models for efficient and effective re-ranking. Our framework enables re-ranking at very high retrieval depths and combines the merits of both lexical and semantic matching via score interpolation. Furthermore, in order to mitigate the limitations of dual-encoders, we tackle two main challenges: Firstly, we improve computational efficiency by either pre-computing representations, avoiding unnecessary computations altogether, or reducing the complexity of encoders. This allows us to considerably improve ranking efficiency and latency. Secondly, we optimize the memory footprint and maintenance cost of indexes; we propose two complementary techniques to reduce the index size and show that, by dynamically dropping irrelevant document tokens, the index maintenance efficiency can be improved substantially.We perform an evaluation to show the effectiveness and efficiency ofFast-Forwardindexes—our method has low latency and achieves competitive results without the need for hardware acceleration, such as GPUs.
Physical and Biological Characterizations of Injectable Thermosensitive Poly(N-Isopropylacrylamide)-Collagen I Hydrogels Intended for Meniscus Repair
Authors: Ke Chunhai , Lu Xuanyuan , Ni Jiahua , Li Ruicong , Chen Qi , Peng Zhaoxiang 
Published: November 2023

There has been an increase in the incidence of meniscus injuries worldwide, as well as growing needs for injectable hydrogels with the potentials to promote in situ meniscal tissue repair. This work developed poly(N-isopropylacrylamide)-collagen I composite hydrogels, with a series of different collagen I contents. The hydrogels were injectable under room temperature and started to solidify around 32°C due to their thermosensitivities, meeting the requirements of the intended applications. The addition of collagen I to the poly(N-isopropylacrylamide) provided physical reinforcement to the hydrogels. Rheological characterizations showed that, under room temperature, the complex viscosity, the storage modulus, and the loss modulus, respectively, increased from

0.71
±
0.35

Pa•s to

110.95
±
23.22

Pa•s, from

3.28
±
2.02

Pa to

658.06
±
128.07

Pa, and from

3.30
±
1.01

Pa to

308.78
±
56.67

Pa, as the collagen I content in the hydrogel increased from 0% to 1%. Cell proliferation tests and high-density culture also revealed that collagen I promoted bioactivity of the hydrogels and induced fibrochondrocyte phenotype of the chondrocytes. The expressions of collagen I protein and collagen I a1 gene in the PNIPAm-0.5Coll group were 3.50-fold and 3.64-fold of those in the PNIPAm group. In contrast, the expressions of collagen II protein and collagen II a1 gene were less prominent (respectively, 2.36-fold and 3.34-fold in the PNIPAm-0.5Coll group compared with the PNIPAm group). This phenotyping was believed to be conducive to the regeneration of meniscal tissues. The findings of this study have provided an important basis for future in vivo studies and clinical applications of this type of composite hydrogels.