bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast splitting algorithms for sparsity-constrained and noisy group testing
Authors: Price Eric , Scarlett Jonathan , Tan Nelvin 
Published: January 2023

Abstract
In group testing, the goal is to identify a subset of defective items within a larger set of items based on tests whose outcomes indicate whether at least one defective item is present. This problem is relevant in areas such as medical testing, DNA sequencing, communication protocols and many more. In this paper, we study (i) a sparsity-constrained version of the problem, in which the testing procedure is subjected to one of the following two constraints: items are finitely divisible and thus may participate in at most $\gamma $ tests; or tests are size-constrained to pool no more than $\rho $ items per test; and (ii) a noisy version of the problem, where each test outcome is independently flipped with some constant probability. Under each of these settings, considering the for-each recovery guarantee with asymptotically vanishing error probability, we introduce a fast splitting algorithm and establish its near-optimality not only in terms of the number of tests, but also in terms of the decoding time. While the most basic formulations of our algorithms require $\varOmega (n)$ storage for each algorithm, we also provide low-storage variants based on hashing, with similar recovery guarantees.
Stratification of PD-1 blockade response in melanoma using pre- and post-treatment immunophenotyping of peripheral blood
Authors: Edner Natalie M , Ntavli Elisavet , Petersone Lina , Wang Chun Jing , Fabri Astrid , Kogimtzis Alexandros , Ovcinnikovs Vitalijs , Ross Ellen M , Heuts Frank , Elfaki Yassin , Houghton Luke P , Talbot Toby , Sheri Amna , Pender Alexandra , Chao David , Walker Lucy S K 
Published: January 2023

SummaryEfficacy of checkpoint inhibitor therapies in cancer varies greatly, with some patients showing complete responses while others do not respond and experience progressive disease. We aimed to identify correlates of response and progression following PD-1-directed therapy by immunophenotyping peripheral blood samples from 20 patients with advanced malignant melanoma before and after treatment with the PD-1 blocking antibody pembrolizumab. Our data reveal that individuals responding to PD-1 blockade were characterised by increased CD8 T cell proliferation following treatment, while progression was associated with an increase in CTLA-4-expressing Treg. Remarkably, unsupervised clustering analysis of pre-treatment T cell subsets revealed differences in individuals that went on to respond to PD-1 blockade compared to individuals that did not. These differences mapped to expression of the proliferation marker Ki67 and the costimulatory receptor CD28 as well as the inhibitory molecules 2B4 and KLRG1. While these results require validation in larger patient cohorts, they suggest that flow cytometric analysis of a relatively small number of T cell markers in peripheral blood could potentially allow stratification of PD-1 blockade treatment response prior to therapy initiation.
Dimension-Free Estimates for the Discrete Spherical Maximal Functions
Authors: Mirek Mariusz , Szarek Tomasz Z , Wróbel Błażej 
Published: January 2023

Abstract
We prove that the discrete spherical maximal functions (in the spirit of Magyar, Stein, and Wainger) corresponding to the Euclidean spheres in $\mathbb {Z}^{d}$ with dyadic radii have $\ell ^{p}(\mathbb {Z}^{d})$ bounds for all $p\in [2, \infty ]$ independent of the dimensions $d\ge 5$. An important part of our argument is the asymptotic formula in the Waring problem for the squares with a dimension-free multiplicative error term. By considering new approximating multipliers, we will show how to absorb an exponential in dimension (like $C^{d}$ for some $C&gt;1$) growth in norms arising from the sampling principle of Magyar, Stein, and Wainger and ultimately deduce dimension-free estimates for the discrete spherical maximal functions.
Development of a Bispecific Antibody Targeting Clinical Isolates of Acinetobacter baumannii
Authors: Nielsen Travis B , Yan Jun , Slarve Matthew , Li Rachel , Junge Jason A , Luna Brian M , Wilkinson Ian , Yerramalla Udaya , Spellberg Brad 
Published: January 2023

Abstract

Background
We previously reported developing 2 anticapsular monoclonal antibodies (mAbs) as a novel therapy for Acinetobacter baumannii infections. We sought to determine whether a bispecific mAb (bsAb) could improve avidity and efficacy while maximizing strain coverage in one molecule.

Methods
Humanized mAb 65 was cloned into a single-chain variable fragment and attached to humanized mAb C8, combining their paratopes into a single bsAb (C73). We tested bsAb C73’s strain coverage, binding affinity, ex vivo opsonic activity, and in vivo efficacy compared to each mAb alone and combined.

Results
The bsAb demonstrated strain coverage, binding affinity, opsonization, and in vivo efficacy superior to either original mAb alone or combined.

Conclusions
A humanized bsAb targeting distinct A. baumannii capsule moieties enabled potent and effective coverage of disparate A. baumannii clinical isolates. The bsAb enhances feasibility of development by minimizing the number of components of a promising novel therapeutic for these difficult-to-treat infections.
Transversal Politics of Big Tech
Authors: Monsees Linda , Liebetrau Tobias , Austin Jonathan Luke , Leander Anna , Srivastava Swati 
Published: January 2023

Abstract
Our everyday life is entangled with products and services of so-called Big Tech companies, such as Amazon, Google, and Facebook. International relations (IR) scholars increasingly seek to reflect on the relationships between Big Tech, capitalism, and institutionalized politics, and they engage with the practices of algorithmic governance and platformization that shape and are shaped by Big Tech. This collective discussion advances these emerging debates by approaching Big Tech transversally, meaning that we problematize Big Tech as an object of study and raise a range of fundamental questions about its politics. The contributions demonstrate how a transversal perspective that cuts across sociomaterial, institutional, and disciplinary boundaries and framings opens up the study of the politics of Big Tech. The discussion brings to the fore perspectives on the ontologies of Big Tech, the politics of the aesthetics and credibility of Big Tech and rethinks the concepts of legitimacy and responsibility. The article thereby provides several inroads for how IR and international political sociology can leverage their analytical engagement with Big Tech and nurture imaginaries of alternative and subversive technopolitical futures.
Emerging resistance inStaphylococcus epidermidisduring dalbavancin exposure: a case report andin vitroanalysis of isolates from prosthetic joint infections
Authors: Al Janabi Jasmina , Tevell Staffan , Sieber Raphael Niklaus , Stegger Marc , Söderquist Bo 
Published: January 2023

AbstractBackgroundDalbavancin, a semisynthetic lipoglycopeptide with exceptionally long half-life and Gram-positive spectrum, is an attractive option for infections requiring prolonged therapy, including prosthetic joint infections (PJIs).ObjectivesTo investigate the prevalence of reduced susceptibility to dalbavancin in a strain collection of Staphylococcus epidermidis from PJIs, and to investigate genomic variation in isolates with reduced susceptibility selected during growth under dalbavancin exposure.MethodsMIC determination was performed on S. epidermidis isolates from a strain collection (n = 64) and from one patient with emerging resistance during treatment (n = 4). These isolates were subsequently cultured on dalbavancin-containing agar and evaluated at 48 h; MIC determination was repeated if phenotypical heterogeneity was detected during growth. Population analysis profile (PAP-AUC) was performed in isolates where a  ≥ 2-fold increase in MIC was detected, together with corresponding parental isolates (n = 21). Finally, WGS was performed.ResultsAll strains grew at 48 h on agar containing 0.125 mg/L dalbavancin. PAP-AUC demonstrated significant differences between parental and derived strains in four of the eight analysed groups. An amino acid change in the walK gene coinciding with emergence of phenotypic resistance was detected in the patient isolates, whereas no alterations were found in this region in the in vitro derived strains.ConclusionsExposure to dalbavancin may lead to reduced susceptibility to dalbavancin through either selection of pre-existing subpopulations, epigenetic changes or spontaneous mutations during antibiotic exposure. Source control combined with adequate antibiotic concentrations may be important to prevent emerging reduced susceptibility during dalbavancin treatment.
QMAC-dRAST for the direct testing of antibiotic susceptibility for Enterobacterales in positive blood-culture broth: a comparison of the performances with the MicroScan system and direct disc diffusion testing methods
Authors: Gallois E , Fihman V , Danjean M , Gomart C , Kimseng H , Le Guen R , Royer G , Woerther P L 
Published: January 2023

AbstractObjectivesTo evaluate the performances of the QMAC-dRAST GN (Gram-negative) kit for rapid antimicrobial sensitivity testing (AST) and two other methods, directly on positive blood-culture broth (PBCB), by comparison with a reference method: the MicroScan method based on broth microdilution on colonies isolated on PBCB subculture.MethodsIn total, 156 samples were collected prospectively from blood cultures positive for a Gram-negative rod. Each sample was tested with four AST techniques: (i) the QMAC dRAST GN kit, (ii) the disc diffusion (DD) method, (iii) the MicroScan method applied directly to PBCB; and (iv) MicroScan with isolates from PBCB subculture, as a reference.ResultsFor 124 PBCB containing Enterobacterales, overall essential agreement (EA) and categorical agreement (CA) between the QMAC-dRAST on PBCB and the reference reached 95.7% and 93.5%, respectively. There were 3.0% very major errors (VME), 4.0% major errors (ME) and 2.8% minor errors (mE). A comparison of MicroScan on PBCB and the reference yielded 98.8% EA, 98.5% CA, and rates of 0.6% VME, 0.9% ME and 0.7% mE. The DD method on PBCB gave a CA of 95.8% and rates of 1.7% for VME, 2.0% for ME and 1.9% for mE. Results were obtained more rapidly for QMAC-dRAST (median of 6 h 37 min versus 18 h for the MicroScan and DD methods on PBCB).ConclusionsThe QMAC-dRAST system provided rapid results well correlated with the reference method on PBCB containing Enterobacterales. Given the shorter time-to-results, the QMAC-dRAST system constitutes a fast and reliable alternative to conventional AST methods.
Antibiotic treatment of respiratory tract infections in adults in Norwegian general practice
Authors: Skow Marius , Fossum Guro H , Høye Sigurd , Straand Jørund , Emilsson Louise , Brænd Anja Maria 
Published: January 2023

Abstract

Objectives
To analyse the prevalence of respiratory tract infection (RTI) episodes with and without antibiotic prescriptions in adult patients in Norwegian general practice during the period 2012–2019.

Methods
Observational study linking data from the Norwegian Control and Payment for Health Reimbursements Database and the Norwegian Prescription Database. Episodes of acute RTIs in patients aged 18 years or older were identified and linked to antibiotic prescriptions dispensed within 7 days after diagnosis. We analysed annual infection rates and antibiotic prescription rates and antibiotics prescribed for the different RTI conditions.

Results
RTI episode rate per 1000 inhabitants was 312 in 2012 and 277 in 2019, but showed no linear trend of change during the study period (P = 0.205). Antibiotic prescription rate decreased from 37% of RTI episodes in 2012 to 23% in 2019 (P &lt; 0.001). The reduction in prescribing was most pronounced for episodes coded with ICPC-2 symptom diagnoses, as well as upper RTIs, influenza, acute bronchitis and sinusitis. Prescriptions for phenoxymethylpenicillin decreased from 178 746 in 2012 to 143 095 in 2019, but increased as proportion of total antibiotic prescriptions from 40% in 2012 to 53% in 2019 (P &lt; 0.001).

Conclusions
This study demonstrates stable RTI episode rates and reduced antibiotic prescription rates for RTIs for adults in Norwegian general practice 2012–2019. We also observed a shift towards relatively more use of phenoxymethylpenicillin and less broad-spectrum antibiotics. These changes are in line with the aims of the Norwegian strategy against antibiotic resistance.
Fidaxomicin to prevent recurrent Clostridioides difficile: what will it cost in the USA and Canada?
Authors: Patel Devangi , Senecal Julien , Spellberg Brad , Morris Andrew M , Saxinger Lynora , Footer Brent W , McDonald Emily G , Lee Todd C 
Published: January 2023

Abstract

Importance
Recent changes in guidelines for managing Clostridioides difficile infections (CDI) have placed fidaxomicin as a first-line treatment.

Objective
To estimate the net cost of first-line fidaxomicin compared to vancomycin in the American and Canadian healthcare systems and to estimate the price points at which fidaxomicin would become cost saving for the prevention of recurrence.

Data sources and study selection
We identified randomized, placebo-controlled trials directly comparing fidaxomicin with vancomycin that reported on recurrence. Medication costs were obtained from the Veterans Affairs Federal Supply Schedule (US) and the Quebec drug formulary (Canada). The average cost of a CDI recurrence was established through a systematic review for each country.

Data extraction, synthesis and outcome measures
For efficacy, data on CDI recurrence at day 40 were pooled using a restricted maximal likelihood random effects model. For the cost review, the mean cost across identified studies was adjusted to reflect May 2022 dollars. These were used to estimate the net cost per recurrence prevented with fidaxomicin and the price point below which fidaxomicin would be cost saving.

Results
The estimated mean system costs of a CDI recurrence were $15 147USD and $8806CAD, respectively. Preventing one recurrence by using first-line fidaxomicin over vancomycin would cost $38 222USD (95%CI $30 577–$57 332) and $13 760CAD (95%CI $11 008–$20 640), respectively. The probability that fidaxomicin was cost saving exceeded 95% if priced below $1140USD or $860CAD, respectively.

Conclusions and Relevance
An increased drug expenditure on fidaxomicin may not be offset through recurrence prevention unless the fidaxomicin price is negotiated.
A call to action—stopping antimicrobial resistance
Authors: Eisinger Robert W , Williams Mark P , Choe Sung Hee , Krofah Esther 
Published: January 2023

Abstract
Antimicrobial resistance is a public health emergency and represents an impending pandemic. Implementing the lessons learned from responding to the COVID-19 pandemic is essential in accelerating the development of new antimicrobials and therapeutic strategies, rapid diagnostics and improved vaccines. A rededicated, coordinated and collaborative global effort of all stakeholders in academia, healthcare, government agencies, industry, finance and philanthropy is essential to halt the continued spread of antimicrobial resistance and to prevent further morbidity and mortality from drug-resistant pathogens.
Methylorubrum rhodesianumM520 as a biocontrol agent againstMeloidogyne incognita(Tylenchida: Heteroderidae) J2s infecting cucumber roots
Authors: Zhao Zhengyang , Wang Lin , Khan Raja Asad Ali , Song Xiaojun , Najeeb Saba , Zhao Jianlong , Yang Yuhong , Ling Jian , Mao Zhenchuan , Jiang Xianzhi , Xie Bingyan , Li Yan 
Published: January 2023

AbstractAimsRoot-knot nematodes (RKNs) are plant pathogens that cause huge economic losses worldwide. The biological management of RKNs may be a sustainable alternative to chemical control methods. Here, the biocontrol potential of Methylorubrum rhodesianum M520 against the RKN Meloidogyne incognita was investigated to theoretically support its application as a biocontrol agent in field production.Methods and resultsIn-vitro assays showed 91.9% mortality of M. incognita second-stage juveniles in the presence of strain M520 and that the hatching rate of M. incognita eggs was 21.7% lower than that of eggs treated with sterile water. In pot experiments, the M520 treatment caused 70.8% reduction in root-knots and increased plant shoot length and stem and root fresh weights, compared to control plant values. In split-root experiments, cucumber roots treated with M520 showed 25.6% decrease in root gall number, compared to that in control roots.ConclusionM520 has multiple mechanisms against RKNs and might be used as a biocontrol agent against M. incognita in cucumber, laying a foundation for further studying M520 biocontrol against RKNs.
StoryboardR: an R package and Shiny application designed to visualize real-world data from clinical patient registries
Authors: Miller David M , Shalhout Sophia Z 
Published: January 2023

Abstract

Objectives
Tumor registries are a rich source of real-world data which can be used to test important hypotheses that inform clinical care. Exploratory data analysis at the level of individual subjects, when enhanced by interactive data visualizations, has the potential to provide novel insights and generate new hypothesis.

Materials and Methods
We created StoryboardR: an R package and Shiny application designed to visualize real-word data from tumor registries.

Results
StoryboardR facilitates the data visualization of real-word data from tumor registries captured in REDCap®. The output is an interactive timeline that allows for a visual interpretation of the relationship between potential prognostic and/or predictive biomarkers and outcomes.

Conclusions
StoryboardR is freely available under the Massachusetts Institute of Technology license and can be obtained from GitHub. StoryboardR is executed in R and deployed as a Shiny application for non-R users. It produces data visualizations of patient journeys from tumor registries.
Evaluation of Heating Times for Loss on Drying at 105°C for Estimation of Laboratory Dry Matter in Animal Feeds
Authors: Quirino Daiana F , Lima Nicole S A , Palma Malber N N , Franco Marcia O , Detmann Edenio 
Published: January 2023

AbstractBackgroundDry matter (DM) is a routine test for all animal feeds, facilitating feed comparisons and diet formulation. It is the most frequent test, yet the most challenging with respect to precision and accuracy.ObjectiveOur objective was to evaluate the accuracy, repeatability, and physicochemical impacts of oven-drying times on LDM test results in animal feeds obtained by loss on drying (LoD) at 105°C.MethodsEighteen primary samples collected from different feed sources were grouped into high-moisture (HM) and low-moisture (LM) content materials. The tested methods were based on LoD at 105°C and Karl Fischer titration was adopted as the reference method. Test portions were oven dried at 105°C for 3, 6, 12, 16, and 24 h, and test results were compared to the reference method. Test portions were also subjected to a color evaluation using a colorimetric technique.ResultsThe method based on 3 h of drying provided the closest estimates to those obtained by Karl Fischer titration. Extending heating time (i.e., above 3 h) increased the bias, especially for HM feeds, which was attributed to a higher occurrence of non-enzymatic reactions. This was corroborated by the color of the residues, which became darker with increased heating time. The repeatability of LoD methods was considered adequate, ranging from 0.32 to 0.73%.ConclusionThe LoD method based on the binomial 105°C × 3 h minimizes the bias in the water recovery and causes less non-enzymatic browning in the test portions.HighlightsThe loss-on-drying method recommended for laboratory DM in animal feeds is drying the test portions at 105°C for 3 h.
3-Nitrooxypropanol supplementation of a forage diet decreased enteric methane emissions from beef cattle without affecting feed intake and apparent total-tract digestibility
Authors: Alemu Aklilu W , Gruninger Robert J , Zhang Xiu Min , O’Hara Eóin , Kindermann Maik , Beauchemin Karen A 
Published: January 2023

Abstract
Supplementation of ruminant diets with the methane (CH4) inhibitor 3-nitrooxypropanol (3-NOP; DSM Nutritional Products, Switzerland) is a promising greenhouse gas mitigation strategy. However, most studies have used high grain or mixed forage-concentrate diets. The objective of this study was to evaluate the effects of supplementing a high-forage diet (90% forage DM basis) with 3-NOP on dry matter (DM) intake, rumen fermentation and microbial community, salivary secretion, enteric gas emissions, and apparent total-tract nutrient digestibility. Eight ruminally cannulated beef heifers (average initial body weight (BW) ± SD, 515 ± 40.5 kg) were randomly allocated to two treatments in a crossover design with 49-d periods. Dietary treatments were: 1) control (no 3-NOP supplementation); and 2) 3-NOP (control + 150 mg 3-NOP/kg DM). After a 16-d diet adaption, DM intake was recorded daily. Rumen contents were collected on days 17 and 28 for volatile fatty acid (VFA) analysis, whereas ruminal pH was continuously monitored from days 20 to 28. Eating and resting saliva production were measured on days 20 and 31, respectively. Diet digestibility was measured on days 38–42 by the total collection of feces, while enteric gas emissions were measured in chambers on days 46–49. Data were analyzed using the mixed procedure of SAS. Dry matter intake and apparent total-tract digestibility of nutrients (DM, neutral and acid detergent fiber, starch, and crude protein) were similar between treatments (P ≥ 0.15). No effect was observed on eating and resting saliva production. Relative abundance of the predominant bacterial taxa and rumen methanogen community was not affected by 3-NOP supplementation but rather by rumen digesta phase and sampling hour (P ≤ 0.01). Total VFA concentration was lower (P = 0.004) following 3-NOP supplementation. Furthermore, the reduction in acetate and increase in propionate molar proportions for 3-NOP lowered (P &lt; 0.001) the acetate to propionate ratio by 18.9% as compared with control (4.1). Mean pH was 0.21 units lower (P &lt; 0.001) for control than 3-NOP (6.43). Furthermore, CH4 emission (g/d) and yield (g/kg DMI) were 22.4 and 22.0% smaller (P &lt; 0.001), respectively, for 3-NOP relative to control. Overall, the results indicate that enteric CH4 emissions were decreased by more than 20% with 3-NOP supplementation of a forage diet without affecting DM intake, predominant rumen microbial community, and apparent total-tract nutrients digestibility.