bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aiding War: Foreign Aid and the Intensity of Violent Armed Conflict
Authors: Findley Michael , Young Joseph K , Strandow Daniel , Cat Olgahan 
Published: July 2023

AbstractDoes foreign aid reduce violence during ongoing wars? In the policy community, there has been growing optimism about the prospect for aid to improve conflict-affected and fragile areas. We investigate whether foreign aid decreases, or even increases, violence during ongoing armed conflict. We advance a theoretical argument that concentrated foreign assistance allocated during ongoing armed conflicts increases military fatalities but decreases civilian fatalities. Using geographically coded data on all sub-Saharan African countries in conflict between 1989 and 2008, within a matching frontier design and supplemented by instrumental variable analysis, we find strong substantive and statistical support for our expectations about military conflict intensity though less support for the expectations about civilian fatalities. The paper provides novel insights about the effects of concentrated aid on military versus civilian conflict intensity, characterizes the effects at a sub-national level, and expands the spatial-temporal period of the analysis. We also probe the plausibility of the causal mechanism using interview evidence drawn from ex-commanders of the Lord’s Resistance Army and generals of the Ugandan People’s Defence Forces in northern Uganda. The paper offers both academic and policy insights, including that foreign aid allocated during ongoing wars may be more problematic than it is helpful.
Pathogenic and transmissional potentials of a Chromobacterium haemolyticum isolate from a hydroponic farm
Authors: Zwe Ye Htut , Li Dan 
Published: July 2023

Abstract

Aims
This study aims to investigate the in vitro pathogenicity of Chromobacterium haemolyticum strain WI5 toward the intestinal tract, its resistance to water treatments, and its potential for foodborne transmission through leafy greens produced in hydroponic systems.

Methods and results
C. haemolyticum WI5 caused cytopathic effects in human colon cells HCT116 and exhibited an 8.2-fold higher cell attachment compared to Salmonella serotype Typhimurium. It showed comparable resistance to sodium hypochlorite (NaOCl) and ultraviolet (UV) treatments as Escherichia coli O157: H7 and Pseudomonas aeruginosa but was more susceptible to desiccation. On lettuce, C. haemolyticum WI5 failed to persist, with counts decreasing below the detection limit (≥4 log reductions) after 3 and 2 days at 4 and 25°C, respectively.

Conclusions
C. haemolyticum WI5 demonstrated considerable virulence features and high in vitro pathogenicity toward the intestinal tract. NaOCl and UV treatments were effective in disinfecting C. haemolyticum in water. Due to its high susceptibility to desiccation and poor survivability on lettuce, the foodborne transmission potential of C. haemolyticum is considered limited.
Evaluation of the Roche MagNA Pure 96 nucleic acid extraction platform for the SPF10 line probe assay system
Authors: Peng Siying , Yin Jian , Liu Yiwei , Bi Zhaofeng , Wu Ting , Qiao Youlin 
Published: July 2023

Abstract

Objective
To evaluate the MagNA Pure 96 (MP96) nucleic acid extraction system as an alternative for cervical specimen processing for human papillomavirus (HPV) genotyping detection by reverse hybridization line probe assay (LiPA-25), compared to the well-established extraction system MagNA Pure LC 2.0 (MPLC).

Methods and results
A total of 200 cervical samples preserved in ThinPrepCyt® solution were extracted by MP96 and MPLC, respectively, and then purified nucleic acids were amplified using the SPF10 PCR primer set. Amplification products were subjected to SPF10-DNA enzyme immunoassay (DEIA) and LiPA-25. The concordance between different extraction methods in this study was reflected in the comparison of the results of the DEIA and LiPA-25. Agreement of HPV-positive results (DEIA) was 97.5% (Kappa = 0.932). Pair-wise analyses of either HPV grouping (any HPV genotypes, any high-risk HPV genotypes, any low-risk HPV genotypes, any nonavalent vaccine-targeted HPV, and any non-vaccine-targeted oncogenic HPV genotypes) identified &gt;95% agreement (all Kappa &gt; 0.900). For the two extraction methods, there was no statistical difference (chi-square test: P = 0.690) for single versus multiple genotypes, and concordant, compatible, and discordant genotypes were observed in 87.0%, 9.5%, and 3.5% of 200 samples, respectively.

Conclusion
HPV genotyping results of the MPLC system and the MP96 system showed a high degree of concordance. Combined with the advantages of high-throughput and anti-contamination of MP96, the MP96 extraction system could be more suitable for the testing of samples in future studies.
Inferring cancer disease response from radiology reports using large language models with data augmentation and prompting
Authors: Tan Ryan Shea Ying Cong , Lin Qian , Low Guat Hwa , Lin Ruixi , Goh Tzer Chew , Chang Christopher Chu En , Lee Fung Fung , Chan Wei Yin , Tan Wei Chong , Tey Han Jieh , Leong Fun Loon , Tan Hong Qi , Nei Wen Long , Chay Wen Yee , Tai David Wai Meng , Lai Gillianne Geet Yi , Cheng Lionel Tim-Ee , Wong Fuh Yong , Chua Matthew Chin Heng , Chua Melvin Lee Kiang , Tan Daniel Shao Weng , Thng Choon Hua , Tan Iain Bee Huat , Ng Hwee Tou 
Published: July 2023

Abstract

Objective
To assess large language models on their ability to accurately infer cancer disease response from free-text radiology reports.

Materials and Methods
We assembled 10 602 computed tomography reports from cancer patients seen at a single institution. All reports were classified into: no evidence of disease, partial response, stable disease, or progressive disease. We applied transformer models, a bidirectional long short-term memory model, a convolutional neural network model, and conventional machine learning methods to this task. Data augmentation using sentence permutation with consistency loss as well as prompt-based fine-tuning were used on the best-performing models. Models were validated on a hold-out test set and an external validation set based on Response Evaluation Criteria in Solid Tumors (RECIST) classifications.

Results
The best-performing model was the GatorTron transformer which achieved an accuracy of 0.8916 on the test set and 0.8919 on the RECIST validation set. Data augmentation further improved the accuracy to 0.8976. Prompt-based fine-tuning did not further improve accuracy but was able to reduce the number of training reports to 500 while still achieving good performance.

Discussion
These models could be used by researchers to derive progression-free survival in large datasets. It may also serve as a decision support tool by providing clinicians an automated second opinion of disease response.

Conclusions
Large clinical language models demonstrate potential to infer cancer disease response from radiology reports at scale. Data augmentation techniques are useful to further improve performance. Prompt-based fine-tuning can significantly reduce the size of the training dataset.
Beta-Binomial Statistical Model for Validation Studies of Analytes with a Binary Response
Authors: LaBudde Robert A , Wehling Paul 
Published: July 2023

Abstract

Background
The probability of detection (POD) model has had widespread application for statistically analyzing single and multiple collaborator validations studies with binary outcome data for a wide range of analytes over the last decade.

Objective
The POD model is placed on a firm theoretical foundation, and extended to a more generalized beta-binomial model.

Methods
The POD model is revisited and embedded in the beta-binomial model. This generalization includes collaborator reproducibility as a specific parameter. The new model includes only two distributional parameters: the overall across-collaborator probability of detection (LPOD) and the intraclass correlation of collaborators (ICC), measuring irreproducibility. Differences between methods are measured by the difference in LPOD values, denoted dLPOD.

Results
Accurate statistical estimators and confidence intervals are provided with validation by simulation. This new beta-binomial model will be applicable to a full range of candidate methods giving binary qualitative results, including microbiological, toxin, allergen, biothreat, and botanical analytes.

Conclusions
The new beta-binomial model provides easy equivalence tests to show the study clearly demonstrates (with 95% confidence) that the method differences and collaborator reproducibility are acceptable.

Highlights
The validation system for qualitative binary methods using probability of detection (POD) of an analyte as the parameter of interest has been modified and further validated.
Topology optimization via machine learning and deep learning: a review
Authors: Shin Seungyeon , Shin Dongju , Kang Namwoo 
Published: July 2023

Abstract
Topology optimization (TO) is a method of deriving an optimal design that satisfies a given load and boundary conditions within a design domain. This method enables effective design without initial design, but has been limited in use due to high computational costs. At the same time, machine learning (ML) methodology including deep learning has made great progress in the 21st century, and accordingly, many studies have been conducted to enable effective and rapid optimization by applying ML to TO. Therefore, this study reviews and analyzes previous research on ML-based TO (MLTO). Two different perspectives of MLTO are used to review studies: (i) TO and (ii) ML perspectives. The TO perspective addresses “why” to use ML for TO, while the ML perspective addresses “how” to apply ML to TO. In addition, the limitations of current MLTO research and future research directions are examined.
Micrococcus spp. as a promising source for drug discovery: A review
Authors: Tizabi Daniela , Hill Russell T 
Published: July 2023

Abstract
Historically, bacteria of the phylum, Actinobacteria have been a very prominent source of bioactive compounds for drug discovery. Among the actinobacterial genera, Micrococcus has not generally been prioritized in the search for novel drugs. The bacteria in this genus are known to have very small genomes (generally &lt; 3 Mb). Actinobacteria with small genomes seldom contain the well-characterized biosynthetic gene clusters such as those encoding polyketide synthases and nonribosomal peptide synthetases that current genome mining algorithms are optimized to detect. Nevertheless, there are many reports of substantial pharmaceutically relevant bioactivity of Micrococcus extracts. On the other hand, there are remarkably few descriptions of fully characterized and structurally elucidated bioactive compounds from Micrococcus spp. This review provides a comprehensive summary of the bioactivity of Micrococcus spp. that encompasses antibacterial, antifungal, cytotoxic, antioxidant, and anti-inflammatory activities. This review uncovers the considerable biosynthetic potential of this genus and highlights the need for a re-examination of these bioactive strains, with a particular emphasis on marine isolates, because of their potent bioactivity and high potential for encoding unique molecular scaffolds.
Policy options to facilitate cancer genomic variant data sharing: outcomes of a modified policy Delphi
Authors: Robinson Jill O , Daoud Amira , Geary Janis , Rahimzadeh Vasiliki , Bollinger Juli , Guerrini Christi J , Cook-Deegan Robert , McGuire Amy L , Majumder Mary A 
Published: July 2023

Abstract
Sharing cancer gene variant and relevant clinical data could accelerate progress in cancer genomics. However, data sharing is currently impeded by issues related to financial sustainability, equity, incentives, privacy and security, and data quality. Evidence-based policy options to facilitate data sharing in these domains, and ultimately improve interpretation of cancer-associated genomic variants, are therefore needed. We conducted a modified policy Delphi with expert stakeholders that involved generating, evaluating, and ranking potential policy options to address these issues, with a focus on the US context. We found policy options in the financial sustainability domain were highly ranked, particularly stable funding for trusted entities. However, some Delphi panelists noted that the culture of public research funding has favored short-term grants. Panelists favored policy options focused on action by funders, which had the highest overall total scores that combined effectiveness and feasibility ratings and priority ranking within domains. Panelists also endorsed some policy options connected to actors such as journals, but they were more skeptical of policy options connected to legislative actors and data resources. These findings are critical inputs for policy makers as they consider policies to enable sharing of cancer gene variant data to improve health.
Estimating default probabilities for no- and low-default portfolios: parameter specification via floor constraints
Authors: Blümke Oliver 
Published: July 2023

AbstractFor low- and no-default portfolios, financial institutions are confronted with the problem to estimate default probabilities for credit ratings for which no default was observed. The Bayesian approach offers a solution but brings the problem of the parameter assignment of the prior distribution. Sequential Bayesian updating allows to settle the question of the location parameter or mean of the prior distribution. This article proposes to use floor constraints to determine the scale or standard deviation parameter of the prior distribution. The floor constraint can also be used to determine the free parameter γ in the Pluto–Tasche approach.
Ageing and quenching through the Ageing Diagram – II. Physical characterization of galaxies
Authors: Corcho-Caballero Pablo , Ascasibar Yago , Cortese Luca , Sánchez Sebastián F , López-Sánchez Ángel R , Fraser-McKelvie Amelia , Zafar Tayyaba 
Published: July 2023

ABSTRACT
The connection between quenching mechanisms, which rapidly turn star-forming systems into quiescent, and the properties of the galaxy population remains difficult to discern. In this work we investigate the physical properties of MaNGA and SAMI galaxies at different stages of their star formation history. Specifically, we compare galaxies with signatures of recent quenching (Quenched) – $\rm H \, \alpha$ in absorption and low Dn(4000) – with the rest of the low star-forming and active population (Retired and Ageing, respectively). The analysis is performed in terms of characteristics such as the total stellar mass, half-light radius, velocity-to-dispersion ratio, metallicity, and environment. We find that the Ageing population comprises a heterogeneous mixture of galaxies, preferentially late-type systems, with diverse physical properties. Retired galaxies, formerly Ageing or Quenched systems, are dominated by early-type high-mass galaxies found both at low and dense environments. Most importantly, we find that recently quenched galaxies are consistent with a population of compact low-mass satellite systems, with higher metallicities than their Ageing analogues. We argue that this is compatible with being quenched after undergoing a star-burst phase induced by environmental processes (e.g. ram pressure). However, we also detect a non-negligible fraction of field central galaxies likely quenched by internal processes. This study highlights that, in order to constrain the mechanisms driving galaxy evolution, it is crucial to distinguish between old (Retired) and recently quenched galaxies, thus requiring at least two estimates of the specific star formation rate over different time-scales.
Detecting the H i power spectrum in the post-reionization Universe with SKA-Low
Authors: Chen Zhaoting , Chapman Emma , Wolz Laura , Mazumder Aishrila 
Published: July 2023

ABSTRACT
We present a survey strategy to detect the neutral hydrogen (H i) power spectrum at 5 &lt; z &lt; 6 using the SKA-Low radio telescope in presence of foregrounds and instrumental effects. We simulate observations of the inherently weak H i signal post-reionization with varying levels of noise and contamination with foreground amplitudes equivalent to residuals after sky model subtraction. We find that blind signal separation methods on imaged data are required in order to recover the H i signal at large cosmological scales. Comparing different methods of foreground cleaning, we find that Gaussian Process Regression (GPR) performs better than Principle Component Analysis (PCA), with the key difference being that GPR uses smooth kernels for the total data covariance. The integration time of one field needs to be larger than ∼250 h to provide large enough signal-to-noise ratio (SNR) to accurately model the data covariance for foreground cleaning. Images within the primary beam field-of-view give measurements of the H i power spectrum at scales $k\sim 0.02\, {\rm Mpc^{-1}}-0.3\, {\rm Mpc^{-1} }$ with SNR ∼2–5 in Δ[log(k/Mpc−1)] = 0.25 bins assuming an integration time of 600 h. Systematic effects, which introduce small-scale fluctuations across frequency channels, need to be ≲ 5 × 10−5 to enable unbiased measurements outside the foreground wedge. Our results provide an important validation towards using the SKA-Low array for measuring the H i power spectrum in the post-reionization Universe.
SCOTCH − search for clandestine optically thick compact H iis
Authors: Patel A L , Urquhart J S , Yang A Y , Moore T J T , Menten K M , Thompson M A , Hoare M G , Irabor T , Breen S L , Smith M D 
Published: July 2023

ABSTRACT
This study uses archival high-frequency continuum data to expand the search for Hypercompact H ii regions and determine the conditions at which they appear, as this stage high mass star formation is short-lived and rare. We use 23 GHz continuum data taken towards methanol masers, which are an excellent signpost for very young embedded high-mass protostars. We have searched for high-frequency, optically thick radio sources to identify HC H ii region candidates. The data cover 128 fields that include 141 methanol masers identified by the Methanol Multibeam (MMB) survey. We have detected 68 high-frequency radio sources and conducted a multiwavelength analysis to determine their nature. This has identified 49 H ii regions, 47 of which are embedded in dense clumps fourteen of which do not have a 5 GHz radio counterpart. We have identified 13 methanol maser sites that are coincident with radio sources that have a steep positive spectral index. The majority of these are not detected in the mid-infrared and have been classified as protostellar or young stellar objects in the literature and we therefore consider to be good HC H ii region candidates, however, further work and higher resolution data are needed to confirm these candidates.
Analysis of the possible satellite contamination in LAMOST-MRS spectra
Authors: Kovalev Mikhail , Hainaut Olivier R , Chen Xuefei , Han Zhanwen 
Published: July 2023

ABSTRACT
We present the detection of false positive double-lined spectroscopic binaries candidates using medium-resolution survey spectra from the one time-domain field of Large Sky Area Multi-Object Fibre Spectroscopic Telescope data release 10. The secondary component in all these binaries has near zero radial velocity and solar-like spectral lines. Highly likely this is light from the semitransparent clouds illuminated by the full Moon. However we also suspect that partially this contamination can be caused by a solar light reflected from the surface of low-orbital artificial satellites launched in the beginning of 2022. We found several possible contaminant candidates using archival orbital data. We propose measures to reduce risk of such contamination for the future observations and methods to find it in archived ones.
The Weighted Toxicity Score: Confirmation of a Simple Metric to Communicate Toxicity in Randomized Trials of Systemic Cancer Therapy
Authors: Jordan Jacob , Maki Robert G 
Published: July 2023

Abstract

Introduction
FDA’s Project Optimus was developed in part to better identify appropriate dose and schedule of cancer therapeutics. The tabular method to summarize patients’ maximum toxicity in a clinical trial does not allow for ready comparison to the treatment’s benefit. In this manuscript, we apply a simple tool, the weighted toxicity score (WTS), to trials involving lung cancer immunotherapy and chemotherapy, as well as those cited in a recent publication as examples of trials that represent successful reduction of the appropriate dose of anti-cancer agents.

Methods
PubMed was queried for randomized controlled trials of therapy involving immune checkpoint inhibitors in lung cancer. Trial data from studies highlighting initial success with dose adjustments after FDA approval also were assembled and analyzed according to the WTS procedure described previously, compared to clinical outcomes data.

Results
The WTS provided, with the clinical outcome(s), a data pair that leads to easy interpretation of the expected benefit versus relative toxicity of studies involving immunotherapy or chemoimmunotherapy in lung cancers. The WTS was consistent with the conclusions of the primary studies, helping to quantitate the toxicity difference between treatments in a previously unavailable way.

Conclusion
The WTS provides a tool to show the cost in toxicity of therapy in a randomized clinical trial, with applicability to studies involving chemotherapy, immunotherapy, or kinase-directed therapy. Inclusion of a running tally of WTS during conduct of a trial could serve as one means to adjust dosing or to provide feedback during data safety monitoring of a clinical trial.
Denosumab in Giant Cell Rich Tumors of Bone: An Open-Label Multicenter Phase II Study
Authors: Lipplaa Astrid , Schreuder Willem H , Pichardo Sarina E C , Gelderblom Hans 
Published: July 2023

Abstract

Background
Since giant cell tumors of bone (GCTB) and other giant cell rich tumors of bone (GCRTB) share the histological presence of osteoclastic giant cells and expression of RANK/RANKL, we hypothesized that GCRTB will respond similarly to denosumab as GCTB. The primary objective of this study was to determine the efficacy of denosumab in patients with GCRTB that have recurred or require morbid surgery.

Methods
In this open-label, multicenter, phase II trial, patients with GCRTB were included (June 2018-March 2020). Recruitment was stopped because of low accrual. Patients received denosumab (120 mg) subcutaneously (SC) on day 1 of every 4-week cycle with a loading dose of 120 mg SC on days 8 and 15.

Results
Three patients were enrolled. One withdrew consent before start of study. The remaining patients had central giant cell granuloma of the jawbone (CGCG). Median treatment duration was 15 cycles (range 12-18). In both subjects, improvement in ossification of lesions was seen. Median follow-up was 28.5 months (range 20-37). One patient developed a recurrence for which surgery was performed.

Conclusion
Due to critical emerging real-world data of denosumab in GCRTBs, the study was prematurely stopped and not supportive of use of denosumab for this indication. (ClinicalTrials.gov Identifier: NCT03605199).