bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cost-effective chart review sampling design to account for phenotyping error in electronic health records (EHR) data
Authors: Yin Ziyan , Tong Jiayi , Chen Yong , Hubbard Rebecca A , Tang Cheng Yong 
Published: September 2021

Abstract

Objectives
Electronic health records (EHR) are commonly used for the identification of novel risk factors for disease, often referred to as an association study. A major challenge to EHR-based association studies is phenotyping error in EHR-derived outcomes. A manual chart review of phenotypes is necessary for unbiased evaluation of risk factor associations. However, this process is time-consuming and expensive. The objective of this paper is to develop an outcome-dependent sampling approach for designing manual chart review, where EHR-derived phenotypes can be used to guide the selection of charts to be reviewed in order to maximize statistical efficiency in the subsequent estimation of risk factor associations.

Materials and Methods
After applying outcome-dependent sampling, an augmented estimator can be constructed by optimally combining the chart-reviewed phenotypes from the selected patients with the error-prone EHR-derived phenotype. We conducted simulation studies to evaluate the proposed method and applied our method to data on colon cancer recurrence in a cohort of patients treated for a primary colon cancer in the Kaiser Permanente Washington (KPW) healthcare system.

Results
Simulations verify the coverage probability of the proposed method and show that, when disease prevalence is less than 30%, the proposed method has smaller variance than an existing method where the validation set for chart review is uniformly sampled. In addition, from design perspective, the proposed method is able to achieve the same statistical power with 50% fewer charts to be validated than the uniform sampling method, thus, leading to a substantial efficiency gain in chart review. These findings were also confirmed by the application of the competing methods to the KPW colon cancer data.

Discussion
Our simulation studies and analysis of data from KPW demonstrate that, compared to an existing uniform sampling method, the proposed outcome-dependent method can lead to a more efficient chart review sampling design and unbiased association estimates with higher statistical efficiency.

Conclusion
The proposed method not only optimally combines phenotypes from chart review with EHR-derived phenotypes but also suggests an efficient design for conducting chart review, with the goal of improving the efficiency of estimated risk factor associations using EHR data.
Toxicological Analysis of Intoxications with Synthetic Cathinones
Authors: Pieprzyca Ewelina , Skowronek Rafał , Czekaj Piotr 
Published: September 2021

Abstract
Synthetic cathinones (SCs) are currently the second largest and the second most frequently seized group of new psychoactive substances. They are sold as replacements for controlled stimulants such as amphetamine, cocaine and 3,4-methylenedioxymethamphetamine. Administration of low doses of SCs can cause euphoria and increased alertness, and administration of high doses or chronic use of cathinones can cause serious adverse effects such as hallucinations, delirium, hyperthermia and tachycardia. In the years 2013–2019 in our practice, as many as 16 different SCs were detected in biological materials. This article lists the observed concentrations in 39 fatal and 18 non-fatal cases, in which a single SC as well as an SC in combination with amphetamine or ethyl alcohol were detected and quantified in biological materials. The quantitative analyses were carried out by liquid chromatography with tandem mass spectrometry. The analyzed cases of taking SCs were associated with intoxication (2 cases), fatal intoxication (36), driving under the influence of drugs (10) and other circumstances (9) such as violence, insulting an officer and holding a hostage. Taking SCs has serious side effects that can lead to multiple organ failure and death. Screening for the presence of SCs in biological materials should be part of the routine course of treatment in intoxication cases, both at the stage of clinical diagnosis and at the stage of forensic toxicological analysis. Ethyl alcohol and amphetamine may contribute to increased SC toxicity. These data could be valuable for further interpretation of other results from toxicological analyses.
Pheromone Deployment Strategies for Mating Disruption of a Vineyard Mealybug
Authors: Daane Kent M , Cooper Monica L , Mercer Nathan H , Hogg Brian N , Yokota Glenn Y , Haviland David R , Welter Stephen C , Cave Frances E , Sial Ashfaq A , Boyd Elizabeth A 
Published: September 2021

Abstract
The mealybug, Planococcus ficus (Signoret), is a primary vineyard pest in California and other grape-growing regions throughout the World. Mating disruption programs are commercially available to manage Pl. ficus, but widespread adoption has been limited, in part, by high costs compared with insecticide programs. To improve mating disruption economic effectiveness, different deployment technologies (passive, aerosol, and microencapsulated formulations) were individually examined. Adult male Pl. ficus captures in pheromone traps and categorical ratings of vine infestation or crop damage suggest that all deployment strategies lowered mealybug densities or damage. Using passive dispensers, deployment rates of 310 and 465 per ha lowered Pl. ficus crop damage similar to 615 per ha, a rate commonly used in commercial operations; reduced rates would lower product and deployment costs. Meso dispensers, containing more a.i., deployed at 35 per ha did not have a treatment impact, but a microencapsulated formulation and aerosol canisters lowered male flight captures and/or crop damage. Male mealybug flight activity was greatest from 0500–1100 hr, which coincided with temperatures &gt;16° and &lt;32°C. These restricted times and temperatures suggest programable dispensers might allow pheromone deployment to coincide only with flight patterns. A large field trial using passive dispensers found greater treatment separation after 3 yr of pheromone deployment. Discrepancies in results among vineyards may be related to Pl. ficus density, but combined results from all trials suggest that different deployment technologies can be used to impact Pl. ficus densities and damage, even at reduced rates, especially with continued use over multiple seasons.
Enhanced extracellular α-amylase production in Brevibacillus choshinensis by optimizing extracellular degradation and folding environment
Authors: Yao Dongbang , Zhang Kang , Zhu Xuyang , Su Lingqia , Wu Jing 
Published: September 2021

Abstract
A strategy for optimizing the extracellular degradation and folding environment of Brevibacillus choshinensis has been used to enhance the extracellular production of recombinant α-amylase. First, a gene (bcp) encoding an extracellular protease and another encoding an extracellular chaperone (prsC) were identified in the genome of B. choshinensis HPD31-SP3. Then, the effect of extracellular protein degradation on recombinant α-amylase production was investigated by establishing a CRISPR/Cas9n system to knock out bcp. The effect of extracellular folding capacity was investigated separately by coexpressing extracellular chaperones genes from different sources (prsA, prsC, prsL, prsQ) in B. choshinensis. The final recombinant strain (BCPPSQ), which coexpressed prsQ in a genetic background lacking bcp, produced an extracellular α-amylase activity of 6940.9 U/ml during shake-flask cultivation. This was 2.1-fold greater than that of the original strain BCWPS (3367.9 U/ml). Cultivation of BCPPSQ in a 3-l fermenter produced an extracellular α-amylase activity of 17925.6 U/ml at 72 h, which was 7.6-fold greater than that of BCWPS (2358.1 U/ml). This strategy demonstrates its great potential in enhancing extracellular α-amylase production in B. choshinensis. What's more, this study provides a strategic reference for improving the extracellular production of other recombinant proteins in B. choshinensis.
Association of renal function with the safety and efficacy of cisplatin plus S-1 therapy and docetaxel plus cisplatin plus S-1 therapy in patients with advanced gastric cancer: an exploratory analysis of JCOG1013
Authors: Hironaka Shuichi , Sadachi Ryo , Machida Nozomu , Iwasa Satoru , Yamada Yasuhide , Sasako Mitsuru , Yoshikawa Takaki , Boku Narikazu , Terashima Masanori 
Published: September 2021

Abstract

Background
Although cisplatin and 5-chloro-2,4-dihydropyrimidine (dihydropyrimidine dehydrogenase inhibitor contained in S-1) are excreted into the urine, it remains unknown how creatinine clearance (CrCl) affects the safety and efficacy of cisplatin plus S-1 and docetaxel plus cisplatin plus S-1 in patients with advanced gastric cancer.

Methods
Among the 741 participants in JCOG1013 comparing cisplatin plus S-1 with docetaxel plus cisplatin plus S-1, 723 with serum creatinine levels ≤1.2 mg/dL were categorized into A1 (CrCl ≥ 80 mL/min), A2 (60 ≤ CrCl &lt;80) and A3 (CrCl &lt; 60) in the cisplatin plus S-1 arm and similarly B1, B2 and B3 in the docetaxel plus cisplatin plus S-1 arm. The initial dose modification by CrCl was pre-specified in the docetaxel plus cisplatin plus S-1 arm but not in the cisplatin plus S-1 arm.

Results
The numbers of patients categorized as A1/A2/A3 and B1/B2/B3 were 169/136/57 and 170/138/53, respectively. In the cisplatin plus S-1 arm, a lower CrCl was associated with higher incidences of grade 4 leukopenia (P = 0.006), neutropenia (P = 0.002), and grade 3/4 anorexia (P = 0.004) and febrile neutropenia (P = 0.049), whereas there was no association in the docetaxel plus cisplatin plus S-1 arm. No significant differences were observed according to CrCl in the overall survival [median: 15.4/15.5/15.4 months in A1/A2/A3 (P = 0.886) and 15.3/13.7/13.7 months in B1/B2/B3 (P = 0.719)], progression-free survival [median: 7.1/6.8/6.2 months in A1/A2/A3 (P = 0.884) and 7.5/7.2/7.8 months in B1/B2/B3 (P = 0.851)] and response rates [58.9/57.8/46.9% in A1/A2/A3 (P = 0.311) and 62.0/61.5/51.5% in B1/B2/B3 (P = 0.362)].

Conclusions
Renal impairment was associated with severe adverse events in cisplatin plus S-1 therapy but not with the efficacy in cisplatin plus S-1 and docetaxel plus cisplatin plus S-1 therapy.
A Theory of Claim Resolution
Authors: Baker Scott , Kornhauser Lewis A 
Published: September 2021

AbstractWe study claim resolution. A claim consists of a global fact and a local fact. The global fact is observed by the principal and the agent. The local fact is observed by the agent alone. The agent resolves the claim; the principal decides whether the agent is more likely wrong or right. The principal and agent can disagree about the weight to accord each fact or the overall evidence threshold. The agent cares whether the principal follows or ignores her advice. We characterize how the equilibrium varies with the nature of disagreement. Despite lacking commitment power, we find that the principal grants the agent decision-making authority over an interval of global facts. Further, we find that the principal can better motivate an agent who excessively weights the local fact than an agent who excessively weights the global fact. The principal strictly prefers the former to the latter even though either would make the same number of errors if granted complete autonomy. (JEL C7, K0, D7, K4, M4)
Anticipated Adjudication: An Analysis of the Judicialization of the US Administrative State
Authors: Limbocker Scott , Resh William G , Selin Jennifer L 
Published: September 2021

AbstractTo preserve democratic accountability, the actions of federal agencies remain subject to review by elected officials in the legislative and executive branches. Yet given the vast scope and complexity of the modern federal government, elected officials cannot possibly intervene in all agency matters. This leaves the courts to evaluate agency actions. Applying Rosenbloom’s separation of powers theory of public administration to Nagel’s theory of power as anticipated exchange, we expect that agencies become more judicialized in response to the courts’ influence. Leveraging novel data on personnel records, agency litigation, and policymaking from 1996 to 2016, we estimate regression models using ordinary least squares to provide an original and systematic account of the courts’ influence on agency personnel and professionalization. We find that agencies become more judicialized with increased exposure to the courts. Our dynamic comparison of the rise and fall of the number of judge-like policymakers within agencies highlights agency responses to judicial procedural preferences and suggests that federal agencies adopt personnel and processes that respond to the institutional perspectives of all three branches of government.
Sexual Orientation and Organizational Justice in the Federal Service: Exploring Differences through an Intersectional Lens
Authors: Lewis Gregory B , Emidy M Blake 
Published: September 2021

Abstract
Lesbian, gay, bisexual, and transgender (LGBT) employees perceive less justice in the federal service than do their heterosexual colleagues. The “double jeopardy” hypothesis suggests that this will be especially true for LGBTs with a second stigmatized identity, but intersectionality theory is less clear about whether being LGBT will have a larger impact on other marginalized groups than on gay white men. Using a series of regression analyses applied to the 2012–15 Federal Employee Viewpoint Survey, we investigate whether differences in organizational justice perceptions between LGBT and heterosexual employees are wider among people with other stigmatized identities. We find strong evidence of compounding effects: LGBT–heterosexual differences in perceptions of organizational justice are larger for women than for men, for people of color than for whites, for employees with than without disabilities, and for those earlier in their careers and at lower levels of the federal hierarchy. Anti-LGBT discrimination disproportionately affects LGBTs in weaker positions in society and the federal service. These findings contribute to the broader fields of public administration and diversity management by incorporating an intersectional framework to understand LGBT perceptions and experiences in public organizations.
All Focus is Contrastive: On Polarity (Verum) Focus, Answer Focus, Contrastive Focus and Givenness
Authors: Goodhue Daniel 
Published: September 2021

AbstractI develop a general theory of focus and givenness that can account for truly contrastive focus, and for polarity focus, including data that are sometimes set apart under the label “verum focus”. I show that polarity focus creates challenges for classic theories of focus (e.g. Rooth 1992, a.o.) that can be dealt with by requiring that all focus marking is truly contrastive, and that givenness deaccenting imposes its own distinct requirement on prominence shifts. To enforce true contrast, I employ innocent exclusion (Fox 2007), which I suggest may impose a general filter on what counts as a valid alternative. A key, novel feature of my account is that focal targets are split into two kinds, those that are contextually supported and those that are constructed ad hoc, and that the presence of a contextually supported target can block the ability to construct an ad hoc target. This enables a novel explanation of the data motivating true contrast, and enables polarity focus to be brought into the fold of a unified and truly contrastive theory of focus. I then compare the account to theories of verum focus that make use of non-focus-based verum operators, and make the argument that the focus account is more parsimonious and has better empirical coverage.
Strategies to decrease COVID-19 vaccine hesitancy for children
Authors: Zakeri Marjan , Li Jieni , Sadeghi Simin D , Essien Ekere J , Sansgiry Sujit S 
Published: September 2021

Abstract

Objectives
This study aims to understand acceptable strategies to enhance the COVID-19 vaccine uptake among mothers who have no intention to vaccinate their children.

Methods
In a cross-sectional study, using an online survey in March 2021, we evaluated the variables within the Health Belief Model (severity, susceptibility, benefits, barriers and cues to action) along with parents’ sociodemographic characteristics, previous COVID-19 infection, job loss due to COVID-19 pandemic and the presence of healthcare workers among the household. Total number of children in the household and their chronic health conditions were also assessed. Multivariable logistic regression was performed to evaluate the intention to vaccinate children against the COVID-19 and associations with other variables.

Key findings
The survey response rate was 32.30% (595/1842). Most of the participants were White (72.1%), 31–40 years old (55.46%) and married or in a cohabiting relationship (90.25). Out of 595 mothers with 3–15 years old children, 38.32% had no intention to vaccinate their children. Top factors associated with intention were perceived susceptibility (P = 0.002), benefits (P &lt; 0.001), barriers (P &lt; 0.001), cues to action (P &lt; 0.001) and the presence of healthcare workers in the household (P = 0.032). The main barriers were concerns about vaccine safety, efficacy and side effects. The strongest cue to action was enough information being provided followed by doctors’ recommendations.

Conclusions
Strategies to increase vaccination for children lie in the process of convincing parents with providing reliable information on the vaccine safety, efficacy and side effects by paediatricians and other healthcare providers.
Prediction of radiation pneumonitis with machine learning using 4D-CT based dose-function features
Authors: Katsuta Yoshiyuki , Kadoya Noriyuki , Mouri Shina , Tanaka Shohei , Kanai Takayuki , Takeda Kazuya , Yamamoto Takaya , Ito Kengo , Kajikawa Tomohiro , Nakajima Yujiro , Jingu Keiichi 
Published: September 2021

Abstract
In this article, we highlight the fundamental importance of the simultaneous use of dose-volume histogram (DVH) and dose-function histogram (DFH) features based on functional images calculated from 4-dimensional computed tomography (4D-CT) and deformable image registration (DIR) in developing a multivariate radiation pneumonitis (RP) prediction model. The patient characteristics, DVH features and DFH features were calculated from functional images by Hounsfield unit (HU) and Jacobian metrics, for an RP grade ≥ 2 multivariate prediction models were computed from 85 non-small cell lung cancer patients. The prediction model is developed using machine learning via a kernel-based support vector machine (SVM) machine. In the patient cohort, 21 of the 85 patients (24.7%) presented with RP grade ≥ 2. The median area under curve (AUC) was 0.58 for the generated 50 prediction models with patient clinical features and DVH features. When HU metric and Jacobian metric DFH features were added, the AUC improved to 0.73 and 0.68, respectively. We conclude that predictive RP models that incorporate DFH features were successfully developed via kernel-based SVM. These results demonstrate that effectiveness of the simultaneous use of DVH features and DFH features calculated from 4D-CT and DIR on functional image-guided radiotherapy.
Loin Pain Hematuria Syndrome—a case report
Authors: Zeb Ehtisham , O'Connor Adam , Sabri Shariq , Muhammad Karim , Qureshi Nafees 
Published: September 2021

Abstract
Loin pain hematuria syndrome (LPHS) is a rare idiopathic condition. LPHS can present with both unilateral and bilateral loin pain, microscopic or macroscopic hematuria. It is a diagnosis of exclusion. The management options for this condition include pain management with narcotics or opioids, renal denervation, kidney autotransplantation and neurectomy or nephrectomy. However, these treatment modalities are the last resort.
A rare case of primary carcinoma of axillary accessory breast tissue
Authors: Sikdar Oishi , Roy Meghna , Al-Ishaq Zaid , Shinde Veena , Sircar Tapan 
Published: September 2021

Abstract
Carcinomas of primary accessory breast tissue are rare, comprising 0.3–0.6% of all breast cancers and occur most commonly in the axilla. We report the unusual case of a 50-year-old lady with mucinous adenocarcinoma of axillary accessory breast tissue. In this report we review the presentation, key investigations and treatment of this condition.
Curating the Syriac Literary Heritage in Egyptian Monasteries: A Newly Identified Numeral System in Syriac (British Library, add. 14587)
Authors: Forness Philip Michael 
Published: September 2021

Abstract
Syriac manuscripts feature several systems of numerals, and earlier studies have identified three based on the Syriac alphabet. Marginal notes found in the manuscript London, British Library, Add. 14587 preserve a fourth and previously undescribed alphabetic numeral system. After presenting this system and discussing the evidence that led to its identification, this article argues on palaeographic grounds that the late eighth century forms a terminus post quem for the numerals found in this manuscript. Analyses of a donation note and another manuscript further suggest that the numerals were added by a monk or monks from the Syriac tradition residing in Egypt, associated with either a monastery in Upper Egypt or the Monastery of the Syrians (Dayr al-Suryan) in Wadi al-Naṭ. In either case, the alphabetic numeral system found in the margins of this manuscript reflects theefforts of Syriac monastic communities in Egypt to curate the Syriac literary heritage and shape the way others encountered it.
Pandemic-related delay of falciparum malaria diagnosis in a traveller leading to cerebral malaria
Authors: Schubert Lorenz , Thurnher Professor Majda M , Machold Professor Klaus , Tobudic Professor Selma , Winkler Professor Stefan 
Published: September 2021

Abstract
We report the case of a 29-year-old male in whom COVID-19 concerns led to a delayed diagnosis of falciparum malaria. The patient developed symptoms of cerebral malaria with cytotoxic lesions of the corpus callosum in magnetic resonance imaging.
Ureides are accumulated similarly in response to UV-C irradiation and wounding in Arabidopsis leaves but are remobilized differently during recovery
Authors: Soltabayeva Aigerim , Bekturova Aizat , Kurmanbayeva Assylay , Oshanova Dinara , Nurbekova Zhadyrassyn , Srivastava Sudhakar , Standing Dominic , Sagi Moshe 
Published: September 2021

Abstract
Purine degradation products have been shown to play roles in plant response to stresses such as drought, salinity, extended dark, nitrogen deficiency, and pathogen infection. In this study, we used Arabidopsis wild-type (WT) and an Atxdh1-knockout mutant defective in xanthine dehydrogenase1 (XDH1) to examine the role of degraded purine metabolites in the responses to wounding or UV-C stress applied to the middle leaves of the plant. Wounding or UV-C stress in the mutant resulted in lower fresh-weight, increased senescence symptoms, and increased cell death compared to WT plants. In addition, WT plants exhibited lower levels of oxidative stress indicators, reactive oxygen species, and malondialdehyde in their leaves than the mutant. Notably, transcripts and proteins functioning in the purine degradation pathway were regulated in such a way that it led to enhanced ureide levels in WT leaves 24h after applying the UV-C or wound stress. However, different remobilization of the accumulated ureides was observed after 72h of stress. In plants treated with UV-C, the concentration of allantoin was highest in young leaves, whereas in wounded plants it was lowest in these leaves and instead accumulated mainly in the middle leaves that had been wounded. These results indicated that in WT plants treated with UV-C, ureides were remobilized from the lower older and damaged leaves to support young leaf growth during the recovery period from stress. After wounding, however, whilst some ureides were remobilized to the young leaves, more remained in the wounded middle leaves to function as antioxidants and/or healing agents.