bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial and Viral Respiratory Tract Microbiota and Host Characteristics in Adults With Lower Respiratory Tract Infections: A Case-Control Study
Authors: Haak Bastiaan W , Brands Xanthe , Davids Mark , Peters-Sengers Hessel , Kullberg Robert F J , van Houdt Robin , Hugenholtz Floor , Faber Daniël R , Zaaijer Hans L , Scicluna Brendon P , van der Poll Tom , Joost Wiersinga W 
Published: June 2021

Abstract

Background
Viruses and bacteria from the nasopharynx are capable of causing community-acquired pneumonia (CAP), which can be difficult to diagnose. We aimed to investigate whether shifts in the composition of these nasopharyngeal microbial communities can be used as diagnostic biomarkers for CAP in adults.

Methods
We collected nasopharyngeal swabs from adult CAP patients and controls without infection in a prospective multicenter case-control study design. We generated bacterial and viral profiles using 16S ribosomal RNA gene sequencing and multiplex polymerase chain reaction (PCR), respectively. Bacterial, viral, and clinical data were subsequently used as inputs for extremely randomized trees classification models aiming to distinguish subjects with CAP from healthy controls.

Results
We enrolled 117 cases and 48 control subjects. Cases displayed significant beta diversity differences in nasopharyngeal microbiota (P = .016, R2 = .01) compared to healthy controls. Our extremely randomized trees classification models accurately discriminated CAP caused by bacteria (area under the curve [AUC] .83), viruses (AUC .95) or mixed origin (AUC .81) from healthy control subjects. We validated this approach using a dataset of nasopharyngeal samples from 140 influenza patients and 38 controls, which yielded highly accurate (AUC .93) separation between cases and controls.

Conclusions
Relative proportions of different bacteria and viruses in the nasopharynx can be leveraged to diagnose CAP and identify etiologic agent(s) in adult patients. Such data can inform the development of a microbiota-based diagnostic panel used to identify CAP patients and causative agents from nasopharyngeal samples, potentially improving diagnostic specificity, efficiency, and antimicrobial stewardship practices.
What to make of the Kaldor-Verdoorn law?
Authors: Basu Deepankar , Budhiraja Manya 
Published: June 2021

Abstract
The Kaldor-Verdoorn law refers to a positive but less than one-for-one causal relationship between the growth rates of output and labour productivity. While empirical research has found that the Kaldor-Verdoorn coefficient lies between 0 and 1, the interpretation of this finding remains unclear. In this paper, we present a model to derive the Kaldor-Verdoorn law. Our results show that the Kaldor-Verdoorn coefficient is jointly determined by the elasticity of factor substitution, labour supply elasticity, the profit share and the increasing returns to scale (or demand-induced technical change) parameter. Hence, estimated Kaldor-Verdoorn coefficients cannot be used, on their own, to infer the presence of aggregate increasing returns to scale—with the exception of the benchmark case of Leontief Production technology (and steady-state analysis coupled with the assumption of Cobb-Douglas production technology). We also report a surprising result: an economy without aggregate increasing returns to scale (or without any demand-induced technical progress) can generate a Kaldor-Verdoorn coefficient that lies between 0 and 1.
Advanced lipoprotein parameters could better explain atheromatosis in non-diabetic chronic kidney disease patients
Authors: Bermudez-Lopez Marcelino , Perpiñan Hector , Amigo Nuria , Castro Eva , Alonso Nuria , Mauricio Didac , Fernandez Elvira , Valdivielso Jose M 
Published: June 2021

ABSTRACT

Background
Chronic kidney disease (CKD) patients have a high burden of atheromatous cardiovascular disease (ASCVD) not fully explained by traditional lipid parameters. Lipoprotein composition and subclass particle number information could improve ASCVD risk assessment. The objective of this study is to investigate the association of advanced lipoprotein parameters with the risk of atheromatosis in a subpopulation of the NEFRONA study.

Methods
This was a cross-sectional study in 395 non-diabetic individuals (209 CKD and 186 non-diabetic and non-CKD) without statin therapy. Vascular ultrasound examination assessing 10 territories was combined with advanced lipoprotein testing performed by nuclear magnetic resonance spectroscopy. Logistic regression was used to estimate adjusted odds ratios (ORs) per 1 standard deviation increment.

Results
Atheromatosis was more prevalent in CKD patients (33.9% versus 64.6%). After adjusting for age, gender, smoking habit and CKD stage, the amount of triglycerides (TGs) within low-density lipoprotein (LDL) lipoproteins was independently and positively associated with atheromatosis [OR 1.33; 95% confidence interval (CI) 1.03–1.74; P = 0.03]. Similarly, total and medium LDL particles (LDL-Ps) showed a positive association (OR 1.29; 95% CI 1.00–1.68; P = 0.05 and OR 1.34; 95% CI 1.04–1.75; P = 0.03, respectively). TG-loaded medium LDL-Ps were higher in CKD patients compared with controls and showed an adjusted OR of 1.40 (95% CI 1.09–1.82; P = 0.01) in non-diabetic patients (CKD and non-CKD individuals). In contrast, non-diabetic CKD patients showed a similar coefficient but the significance was lost (OR 1.2; 95% CI 0.8–1.7; P = 0.359).

Conclusions
Non-diabetic CKD patients showed a higher amount of TG-loaded medium LDL-Ps compared with controls. These particles were independently associated with atheromatosis in non-diabetic patients.
Towards a Global Englishes-aware National English Curriculum of China
Authors: Liu Haibo , Fang Fan 
Published: June 2021

Abstract
Although researchers and practitioners have discussed the concept of Global Englishes (GE), the degree of GE’s influence in the practical use of English is much wider and deeper in the real world than in the field of education. Mainstream ELT practices tend to adhere to native and fixed norms, which are regarded as the central problems in ELT from the perspective of the GE paradigm. Although a GE-oriented pedagogy has been discussed, studies on curriculum in the Chinese ELT context from the GE perspective are relatively rare. This paper aims to investigate the extent to which the National English Curriculum (NEC) in China reflects GE-oriented phonology and cultural learning. The study adopted a content analysis in which the NEC statements on phonology and cultural aspects were identified and discussed. After reporting the findings, the paper further discusses some pedagogic implications about curriculum and language teaching from the GE perspective.
Diversity, properties and functions of bacterial arginases
Authors: Hernández Victor M , Arteaga Alejandra , Dunn Michael F 
Published: June 2021

AbstractThe metalloenzyme arginase hydrolyzes l-arginine to produce l-ornithine and urea. In bacteria, arginase has important functions in basic nitrogen metabolism and redistribution, production of the key metabolic precursor l-ornithine, stress resistance and pathogenesis. We describe the regulation and specific functions of the arginase pathway as well as summarize key characteristics of related arginine catabolic pathways. The use of arginase-derived ornithine as a precursor molecule is reviewed. We discuss the biochemical and transcriptional regulation of arginine metabolism, including arginase, with the latter topic focusing on the RocR and AhrC transcriptional regulators in the model organism Bacillus subtilis. Finally, we consider similarities and contrasts in the structure and catalytic mechanism of the arginases from Bacillus caldovelox and Helicobacter pylori. The overall aim of this review is to provide a panorama of the diversity of physiological functions, regulation and biochemical features of arginases in a variety of bacterial species.
Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex
Authors: Hanson Sara J , Cinnéide Eoin Ó , Salzberg Letal I , Wolfe Kenneth H , McGowan Jamie , Fitzpatrick David A , Matlin Kate 
Published: June 2021

Abstract
The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the O. polymorpha species complex, including representatives of the species O. polymorpha, Ogataea parapolymorpha, Ogataea haglerorum, and Ogataea angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.
The presence and outcome of biliary sphincter disorders in liver-transplant recipients according to the Rome IV classification
Authors: Fernandez-Simon Alejandro , Sendino Oriol , Chavez-Rivera Karina , Córdova Henry , Colmenero Jordi , Crespo Gonzalo , Fundora Yilliam , Samaniego Franco , Ruiz Pablo , Fondevila Constantino , Navasa Miquel , Cárdenas Andrés 
Published: June 2021

Abstract

Background
Biliary sphincter disorders after liver transplantation (LT) are poorly described. We aim to describe the presence and outcome of patients with papillary stenosis (PS) and functional biliary sphincter disorders (FBSDs) after LT according to the updated Rome IV criteria.

Methods
We reviewed all endoscopic retrograde cholangiopancreatographies (ERCPs) performed in LT recipients between January 2003 and December 2019. Information on clinical and endoscopic findings was obtained from electronic health records and endoscopy databases. Laboratory and clinical findings were collected at the time of ERCP and 1 month after ERCP.

Results
Among the 1,307 LT recipients, 336 underwent 849 ERCPs. Thirteen (1.0%) patients met the updated Rome IV criteria for PS [former sphincter of Oddi dysfunction (SOD) type I] and 14 patients (1.0%) met the Rome IV criteria for FBSD (former SOD type II). Biliary sphincterotomy was performed in 13 PS and 10 FBSD cases. One month after sphincterotomy, bilirubin, gamma-glutamyl transferase and alkaline phosphatase levels decreased in 85%, 61%, and 92% of those in the PS group (P = 0.019, 0.087, and 0.003, respectively) and in 50%, 70%, and 80% of those in the FBSD group (P = 0.721, 0.013, and 0.093, respectively). All the 14 patients initially suspected of having a FBSD turned out to have a different diagnosis during the follow-up.

Conclusions
PS after LT is uncommon and occurs in only 1% of LT recipients. Our data do not support the presence of an FBSD after LT. Sphincterotomy is a safe and effective procedure in LT recipients with PS.
Robust instance-optimal recovery of sparse signals at unknown noise levels
Authors: Petersen Hendrik Bernd , Jung Peter 
Published: June 2021

Abstract
We consider the problem of sparse signal recovery from noisy measurements. Many of frequently used recovery methods rely on some sort of tuning depending on either noise or signal parameters. If no estimates for either of them are available, the noisy recovery problem is significantly harder. The square root LASSO and the least absolute deviation LASSO are known to be noise-blind, in the sense that the tuning parameter can be chosen independent on the noise and the signal. We generalize those recovery methods to the rLASSO and give a recovery guarantee once the tuning parameter is above a threshold. Moreover, we analyze the effect of mistuning on a theoretic level and prove the optimality of our recovery guarantee. Further, for Gaussian matrices, we give a refined analysis of the threshold of the tuning parameter and proof a new relation of the tuning parameter on the dimensions. Indeed, for a certain amount of measurements, the tuning parameter becomes independent on the sparsity. Finally, we verify that the least absolute deviation LASSO can be used with random walk matrices of uniformly at random chosen left regular biparitite graphs.
A projector-based approach to quantifying total and excess uncertainties for sketched linear regression
Authors: Chi Jocelyn T , Ipsen Ilse C F 
Published: June 2021

AbstractLinear regression is a classic method of data analysis. In recent years, sketching—a method of dimension reduction using random sampling, random projections or both—has gained popularity as an effective computational approximation when the number of observations greatly exceeds the number of variables. In this paper, we address the following question: how does sketching affect the statistical properties of the solution and key quantities derived from it? To answer this question, we present a projector-based approach to sketched linear regression that is exact and that requires minimal assumptions on the sketching matrix. Therefore, downstream analyses hold exactly and generally for all sketching schemes. Additionally, a projector-based approach enables derivation of key quantities from classic linear regression that account for the combined model- and algorithm-induced uncertainties. We demonstrate the usefulness of a projector-based approach in quantifying and enabling insight on excess uncertainties and bias-variance decompositions for sketched linear regression. Finally, we demonstrate how the insights from our projector-based analyses can be used to produce practical sketching diagnostics to aid the design of judicious sketching schemes.
A set-valued approach applied to a control problem of tuberculosis with treatment
Authors: Boujallal Lahoucine , Balatif Omar , Elhia Mohamed 
Published: June 2021

AbstractThe objective of this paper is to propose a set-valued approach to handle the control problem of tuberculosis (TB) infection model with treatment. The governed model consists of four ordinary differential equations, namely, susceptible, latent, infected and treated individuals. The infectious TB groups are decreased to zero by using a Lyapunov function in the sense of viability theory. The corresponding control laws are given via a continuous selection of an adequately designed feedback map. Furthermore, minimal control is derived via minimal selection of the feedback map, despite its discontinuity. Ultimately, some numerical simulations are presented to show the efficiency of the set-valued approach.
Homogeneous multigrid for HDG
Authors: Lu Peipei , Rupp Andreas , Kanschat Guido 
Published: June 2021

Abstract
We introduce a multigrid method that is homogeneous in the sense that it uses the same hybridizable discontinuous Galerkin (HDG) discretization scheme for Poisson’s equation on all levels. In particular, we construct a stable injection operator and prove optimal convergence of the method under the assumption of elliptic regularity. Numerical experiments underline our analytical findings.
Comparison of Bioassays Used to Determine Onion Thrips (Thysanoptera: Thripidae) Susceptibility to Spinetoram
Authors: Yannuzzi Isabella M , Moretti Erica A , Nault Brian A 
Published: June 2021

AbstractOnion thrips (Thrips tabaci Lindeman) is one of onion’s most damaging insect pests and has a history of developing resistance across insecticide classes. The susceptibility of T. tabaci populations to insecticides can be determined using laboratory bioassays. Three types of bioassays have been documented in the literature specifically for use with T. tabaci: vial assay (contact only), feeding assay (ingestion only), and leaf-dip assay (contact + ingestion). The objectives of this study were to 1) compare insecticide susceptibility levels of a T. tabaci population using these three assays and 2) determine which bioassay’s results were most similar to those generated from exposing thrips to whole plants treated with insecticide. All experiments were conducted using a colony of T. tabaci known to be susceptible to insecticides and all were evaluated for their susceptibility to spinetoram (Radiant SC). Results indicated that 1) each bioassay generated a unique concentration-mortality relationship and LC50 value (0.01, 0.03 and 1.6 ppm for leaf-dip, vial, and feeding assays, respectively), and 2) all bioassays overestimated the susceptibility of the population relative to the whole-plant assay (LC50 = 5.3 ppm). Attributes of these bioassays are discussed relative to their future use in insecticide resistance monitoring programs for T. tabaci.
Mosquitoes (Diptera: Culicidae) from Villages and Forest Areas of Rural Communes in Khanh Hoa and Binh Phuoc Provinces, Vietnam
Authors: Vu Nam S , Hertz Jeffrey C , Martin Nicholas J , Tran Tu C , Fiorenzano Jodi M , Tran Phong V , Nguyen Hoang V , Dang Anh D , Tran Duong N , Motoki Maysa T 
Published: June 2021

Abstract
This study presents the diversity of mosquitoes collected from communes, endemic with malaria and dengue, located in Khanh Hoa and Binh Phuoc Provinces, Vietnam. A total of 10,288 mosquitoes were collected in the village and forested sites using standard larval dippers, cow-baited traps, ultra-violet light traps, and mechanical aspirators. Mosquito taxa were identified morphologically and species complexes/groups were further characterized molecularly. Five genera of mosquitoes were morphologically identified: Anopheles Meigen (21 species), Aedes Meigen (2 species), Culex Linnaeus (5 species), Mansonia Blanchard sp., and Armigeres Theobald sp. The PCR-based identification methods allowed the distinction of members of Maculatus Group, Funestus Group, and Dirus Complex; and DNA barcodes enabled the further identification of the Barbirostris Complex. Data reported here include the first report of An. saeungae Taai & Harbach and An. wejchoochotei Taai & Harbach from Vietnam, and re-emphasizes the significance of using molecular data in an integrated systematic approach to identify cryptic species and better understand their role in disease transmission.
Evaluation of a Methoprene Aerial Application for the Control of Culiseta melanura (Diptera: Culicidae) in Wetland Larval Habitats
Authors: Burtis James C , Poggi Joseph D , Duval Todd B , Bidlack Ellen , Shepard John J , Matton Priscilla , Rossetti Ross , Harrington Laura C 
Published: June 2021

Abstract
Eastern equine encephalitis virus (EEEV) is an arbovirus endemic to the eastern United States. Human cases are rare but can be serious. The primary enzootic vector is Culiseta melanura (Coquillett) (Diptera: Culicidae), an ornithophagic mosquito. We conducted an aerial application of a granular methoprene formulation in Hockomock Swamp (Massachusetts), which represents a focus of EEEV transmission. Water collected from inside and outside Cs. melanura crypts was evaluated in bioassays of early fourth instar Cs. melanura larvae using treated and untreated water. Adult eclosion rates were 36% significantly lower in treated compared with untreated water (P &lt; 0.05). Eclosion rates for water collected from inside crypts were significantly higher (62%) than rates from outside crypts (30%) (P &lt; 0.05), indicating higher efficacy outside crypts. We tested whether reduced methoprene efficacy inside the crypts was due to reduced chemical penetration into this habitat. Chemical water analyses confirmed that methoprene concentrations were lower inside the crypts (0.1 ± 0.05 ppb) compared to water from outside crypts (1.79 ± 0.41 ppb). The susceptibility of Cs. melanura to methoprene was also determined to allow for comparison against concentrations observed in water collected from the field (LC-95: 1.95 ± 0.5 ppb). Overall, methoprene-treated water prevented mosquito development for up to 4 wk, but with a reduction in efficacy between 4- and 6-wk post-application. Our results suggest that aerial methoprene applications can effectively treat open water in wetlands but may not provide efficacious control of Cs. melanura due to an inability to penetrate larval habitats.
PROMETHEUS BOUND?—THE UNCERTAIN FUTURE OF THE UNILATERAL EFFECTS ANALYSIS IN EU MERGER CONTROL AFTER CK TELECOMS
Authors: Deutscher Elias 
Published: June 2021

Abstract
In the recent CK Telecoms (Case T-399/16) judgment, the General Court annulled the European Commission’s decision to block the four-to-three telecom merger Hutchison3G UK/Telefónica UK. This watershed case is set to curtail the Commission’s ability to challenge future mergers in concentrated markets and proposes a fundamental reshape of the analysis of unilateral effects in the absence of dominance. This article shows that CK Telecoms advances six propositions that form the foundation of a new frame of reference for the analysis of unilateral effects under the EU Merger Regulation. This new framework has been welcomed by commentators as a long-overdue recognition that ‘the law’ trumps the Commission’s administrative discretion and as a vindication of the ‘more economic approach’. Based on a thorough review of 15 years of merger enforcement in the mobile telecommunication sector, this article challenges this account by debunking both the ‘rule of law’ and the ‘more economic approach’ arguments in support of the new framework. It instead demonstrates that each of the six principles advanced by CK Telecoms neither constitutes a reaffirmation of ‘the law’, nor aligns EU merger enforcement with the economic analysis of unilateral effects. In critically reflecting on the new framework laid down in CK Telecoms, this article formulates a number of policy proposals as building blocks for an alternative frame of reference that would preserve the effectiveness of EU merger enforcement in future unilateral effects cases while enhancing legal certainty.
‘It’s complicated’: Professional opacity, duality, and ambiguity—A response to Noordegraaf (2020)
Authors: Alvehus Johan , Avnoon Netta , Oliver Amalya L 
Published: June 2021

AbstractIn this comment to Noordegraaf’s ‘Protective or connective professionalism? How connected professionals can (still) act as autonomous and authoritative experts’, we argue that Noordegraaf has contributed significant insights into the development of contemporary professionalism. However, we argue for a less binary and more complex view of forms of professionalism, and for finding ways of understanding professionalism grounded in a relational view of everyday professional work. The first section (by Johan Alvehus) suggests that Noordegraaf’s ‘connective professionalism’ is primarily about new ways of strengthening professionalism’s protective shields by maintaining functional ambiguity and transparent opacity around professional jurisdictions. The second section (by Amalya Oliver and Netta Avnoon) argues for viewing professionalism on a range of protection–connection and offers an approach for understanding how connective and protective models co-occur. Both commentaries thus take a relational, dynamic, and somewhat skeptical view on the reproduction and maintenance of professionalism.