bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-task bioassay pre-training for protein-ligand binding affinity prediction
Authors: Yan Jiaxian , Ye Zhaofeng , Yang Ziyi , Lu Chengqiang , Zhang Shengyu , Liu Qi , Qiu Jiezhong 
Published: December 2023

Abstract
Protein–ligand binding affinity (PLBA) prediction is the fundamental task in drug discovery. Recently, various deep learning-based models predict binding affinity by incorporating the three-dimensional (3D) structure of protein–ligand complexes as input and achieving astounding progress. However, due to the scarcity of high-quality training data, the generalization ability of current models is still limited. Although there is a vast amount of affinity data available in large-scale databases such as ChEMBL, issues such as inconsistent affinity measurement labels (i.e. IC50, Ki, Kd), different experimental conditions, and the lack of available 3D binding structures complicate the development of high-precision affinity prediction models using these data. To address these issues, we (i) propose Multi-task Bioassay Pre-training (MBP), a pre-training framework for structure-based PLBA prediction; (ii) construct a pre-training dataset called ChEMBL-Dock with more than 300k experimentally measured affinity labels and about 2.8M docked 3D structures. By introducing multi-task pre-training to treat the prediction of different affinity labels as different tasks and classifying relative rankings between samples from the same bioassay, MBP learns robust and transferrable structural knowledge from our new ChEMBL-Dock dataset with varied and noisy labels. Experiments substantiate the capability of MBP on the structure-based PLBA prediction task. To the best of our knowledge, MBP is the first affinity pre-training model and shows great potential for future development. MBP web-server is now available for free at: https://huggingface.co/spaces/jiaxianustc/mbp.
Benchmarking and improving the performance of variant-calling pipelines with RecallME
Authors: Vozza Gianluca , Bonetti Emanuele , Tini Giulia , Favalli Valentina , Frigè Gianmaria , Bucci Gabriele , De Summa Simona , Zanfardino Mario , Zapelloni Francesco , Mazzarella Luca 
Published: December 2023

Abstract

Motivation
The steady increment of Whole Genome/Exome sequencing and the development of novel Next Generation Sequencing-based gene panels requires continuous testing and validation of variant calling (VC) pipelines and the detection of sequencing-related issues to be maintained up-to-date and feasible for the clinical settings. State of the art tools are reliable when used to compute standard performance metrics. However, the need for an automated software to discriminate between bioinformatic and sequencing issues and to optimize VC parameters remains unmet.

Results
The aim of the current work is to present RecallME, a bioinformatic suite that tracks down difficult-to-detect variants as insertions and deletions in highly repetitive regions, thus providing the maximum reachable recall for both single nucleotide variants and small insertion and deletions and to precisely guide the user in the pipeline optimization process.

Availability and implementation
Source code is freely available under MIT license at https://github.com/mazzalab-ieo/recallme. RecallME web application is available at https://translational-oncology-lab.shinyapps.io/recallme/. To use RecallME, users must obtain a license for ANNOVAR by themselves.
Is the Party Really Over? Parties, Partisanship and the Politics of Crime
Authors: Guiney Thomas 
Published: December 2023

Abstract
Political parties occupy a contradictory position in the criminological literature: at once active participants in the political contestation of crime but virtually absent from contemporary debates concerning the relationship between crime and democratic theory. In this paper, I present a ‘rational reconstruction’ of party and partisanship as distinctive modes of political association that are vital to liberal democratic systems that take seriously (1) the value of political pluralism and (2) the limits of public reason to yield definitive answers to the crime question. Currently, political parties are failing to perform these mediating roles satisfactorily and I conclude that a stronger normative commitment to an ‘ethic of partisanship’ can help to revitalize our representative democracies and foster a better politics of crime.
CD133-containing microvesicles promote cancer progression by inducing M2-like tumor-associated macrophage polarization in the tumor microenvironment of colorectal cancer
Authors: Kim Sang Yun , Park Sungyeon , Kim Suhyun , Ko Jesang 
Published: December 2023

Abstract
Tumor-associated macrophages (TAMs) are among the most abundant cell types in the tumor microenvironment (TME). The immunosuppressive TME formed by TAMs is an essential prerequisite for cancer progression. Tumor-derived microvesicles (MVs), a subtype of extracellular vesicle shed directly from the plasma membrane, are important regulators of intercellular communication and TME modulation during tumorigenesis. However, the exact mechanism by which tumor-derived MVs induce the generation of the immunosuppressive TME and polarization of TAMs remains unclear. Here, we investigated the role of CD133-containing MVs derived from colorectal cancer (CRC) cells in macrophage polarization and cancer progression. CD133-containing MVs from CRC cells were incorporated into macrophages, and M0 macrophages were morphologically transformed into M2-like TAMs. CD133-containing MVs were found to increase the mRNA expression of M2 macrophage markers. Additionally, cytokine array analysis revealed that M2-like TAMs induced by CD133-containing MVs increased the secretion of interleukin 6, which activated the STAT3 pathway in CRC cells. Furthermore, the conditioned medium of M2-like TAMs promoted cell motility, epithelial–mesenchymal transition, and cell proliferation. However, MVs from CD133-knockdown cells had little effect on TAM polarization and CRC progression. These results demonstrate that CD133-containing MVs induce M2-like TAM polarization and contribute to cancer progression by mediating crosstalk between tumor cells and TAMs in the TME of CRC.
miR-222 inhibits pathological cardiac hypertrophy and heart failure
Authors: Liu Xiaojun , Li Haobo , Hastings Margaret H , Xiao Chunyang , Damilano Federico , Platt Colin , Lerchenmüller Carolin , Zhu Han , Wei Xin Paul , Yeri Ashish , Most Patrick , Rosenzweig Anthony 
Published: December 2023

Abstract

Aims
Physiological cardiac hypertrophy occurs in response to exercise and can protect against pathological stress. In contrast, pathological hypertrophy occurs in disease and often precedes heart failure. The cardiac pathways activated in physiological and pathological hypertrophy are largely distinct. Our prior work demonstrated that miR-222 increases in exercised hearts and is required for exercise-induced cardiac hypertrophy and cardiomyogenesis. Here, we sought to define the role of miR-222 in pathological hypertrophy.

Methods and results
We found that miR-222 also increased in pathological hypertrophy induced by pressure overload. To assess its functional significance in this setting, we generated a miR-222 gain-of-function model through cardiac-specific constitutive transgenic miR-222 expression (TgC-miR-222) and used locked nucleic acid anti-miR specific for miR-222 to inhibit its effects. Both gain- and loss-of-function models manifested normal cardiac structure and function at baseline. However, after transverse aortic constriction (TAC), miR-222 inhibition accelerated the development of pathological hypertrophy, cardiac dysfunction, and heart failure. Conversely, miR-222-overexpressing mice had less pathological hypertrophy after TAC, as well as better cardiac function and survival. We identified p53-up-regulated modulator of apoptosis, a pro-apoptotic Bcl-2 family member, and the transcription factors, Hmbox1 and nuclear factor of activated T-cells 3, as direct miR-222 targets contributing to its roles in this context.

Conclusion
While miR-222 is necessary for physiological cardiac growth, it inhibits cardiac growth in response to pressure overload and reduces adverse remodelling and cardiac dysfunction. These findings support the model that physiological and pathological hypertrophy are fundamentally different. Further, they suggest that miR-222 may hold promise as a therapeutic target in pathological cardiac hypertrophy and heart failure.
Successful β-blocker introduction under intra-aortic balloon pumping and ivabradine in a patient with new-onset dilated cardiomyopathy and pulsus alternans: a case report
Authors: Kashimura Takeshi , Ishizuka Mitsuo , Tanaka Komei , Inomata Takayuki 
Published: December 2023

Abstract

Background
Pulsus alternans has been considered a sign of poor prognosis in patients undergoing treatments for heart failure. However, it may be overlooked in patients with intra-aortic balloon pumps (IABPs). The use of IABP and ivabradine for a β-blocker introduction in a patient with dilated cardiomyopathy (DCM) and pulsus alternans and its consequence have never been reported.

Case summary
In a 16-year-old high school boy with idiopathic DCM [left ventricular end-diastolic diameter (LVDd), 72 mm; left ventricular ejection fraction (LVEF), 18%], the introduction of carvedilol therapy failed, causing cardiogenic shock under inotropes. Therefore, an IABP support was provided, and he was transferred to our hospital. The arterial pressure waveform under IABP demonstrated pulsus alternans with sinus tachycardia at 135/min. Ivabradine reduced the heart rate to ∼100/min and eliminated the pulsus alternans neither decreasing the cardiac index nor increasing the pulmonary artery wedge pressure. Subsequently, carvedilol was reintroduced, and IABP and inotropes were discontinued. Then, 112 days after his transfer to our hospital, left ventricular reverse remodelling was confirmed (LVDd, 54 mm; LVEF, 44%), and he returned to school. The carvedilol dose reached 20 mg/day in 4 months after discharge, and further improvement was observed a year after discharge (LVDd, 54 mm; LVEF, 52%).

Discussion
Pulsus alternans is considered a predictor of poor prognosis. However, IABP and ivabradine may stabilize the haemodynamics in pulsus alternans, leading to a successful β-blocker introduction.
Nurse-led home-based detection of cardiac dysfunction by ultrasound: results of the CUMIN pilot study
Authors: Tromp Jasper , Sarra Chenik , Nidhal Bouchahda , Mejdi Ben Messaoud , Zouari Fourat , Hummel Yoran , Mzoughi Khadija , Kraiem Sondes , Fehri Wafa , Gamra Habib , Lam Carolyn S P , Mebazaa Alexandre , Addad Faouzi 
Published: December 2023

Abstract

Aims
Access to echocardiography is a significant barrier to heart failure (HF) care in many low- and middle-income countries. In this study, we hypothesized that an artificial intelligence (AI)-enhanced point-of-care ultrasound (POCUS) device could enable the detection of cardiac dysfunction by nurses in Tunisia.

Methods and results
This CUMIN study was a prospective feasibility pilot assessing the diagnostic accuracy of home-based AI-POCUS for HF conducted by novice nurses compared with conventional clinic-based transthoracic echocardiography (TTE). Seven nurses underwent a one-day training program in AI-POCUS. A total of 94 patients without a previous HF diagnosis received home-based AI-POCUS, POC N-terminal pro-B-type natriuretic peptide (NT-proBNP) testing, and clinic-based TTE. The primary outcome was the sensitivity of AI-POCUS in detecting a left ventricular ejection fraction (LVEF) &lt;50% or left atrial volume index (LAVI) &gt;34 mL/m2, using clinic-based TTE as the reference. Out of seven nurses, five achieved a minimum standard to participate in the study. Out of the 94 patients (60% women, median age 67), 16 (17%) had an LVEF &lt; 50% or LAVI &gt; 34 mL/m2. AI-POCUS provided an interpretable LVEF in 75 (80%) patients and LAVI in 64 (68%). The only significant predictor of an interpretable LVEF or LAVI proportion was the nurse operator. The sensitivity for the primary outcome was 92% [95% confidence interval (CI): 62–99] for AI-POCUS compared with 87% (95% CI: 60–98) for NT-proBNP &gt; 125 pg/mL, with AI-POCUS having a significantly higher area under the curve (P = 0.040).

Conclusion
The study demonstrated the feasibility of novice nurse–led home-based detection of cardiac dysfunction using AI-POCUS in HF patients, which could alleviate the burden on under-resourced healthcare systems.
Sanctions and the exchange rate in time
Authors: Eichengreen Barry , Ferrari Minesso Massimo , Mehl Arnaud , Vansteenkiste Isabel , Vicquéry Roger 
Published: December 2023

SUMMARY
We test the predictions of recent theoretical studies of the impact of sanctions on the exchange rate. We build a database of exchange rates and sanctions spanning 1914–45 – an era when both large and small economies were targeted by multilateral sanction packages, facilitating comparisons with today’s Russian war episode. We estimate the dynamic response of the exchange rate in a panel of sanction episodes at weekly frequency using local projections, conditioning on the type of sanctions taken. We tease out mechanisms through which sanctions affect the exchange rate by estimating their effects on macroeconomic variables plausibly acting as transmission channels. Our estimates suggest that import restrictions, export restrictions, asset freezes and trade embargoes lead to exchange rate effects consistent with theory, though the precision of the measured effects varies across sanction type. These findings suggest that recent models of the effects of sanctions on the exchange rate do not just match developments in today’s specific Russia episode but have broader applicability. It follows that the direction of exchange rate movements is not an adequate metric of the success or failure of sanctions but a reflection of the type and scale of the measures taken.
Root colonization by beneficial rhizobacteria
Authors: Liu Yunpeng , Xu Zhihui , Chen Lin , Xun Weibing , Shu Xia , Chen Yu , Sun Xinli , Wang Zhengqi , Ren Yi , Shen Qirong , Zhang Ruifu 
Published: December 2023

Abstract
Rhizosphere microbes play critical roles for plant’s growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.
Microbial populations, sensory, and volatile compounds profiling of local cooked rice
Authors: Mohammad Sabri Nur-Shahera , Mahyudin Nor Ainy , Abdullah Sani Muhammad Shirwan , Han Ming Gan , Chong Kah Hui , Padmanabhan Kousalya , Shan Jiang , Mahmud Ab Rashid Nor Khaizura 
Published: December 2023

Abstract

Objectives
This study is designed to investigate the microbial populations, sensory, and volatile compounds profiling of locally cooked rice stored at room temperature (30 °C) on days 0, 1, 2, and 3 (D0, D1, D2, and D3) for the determination of specific spoilage organisms (SSOs).

Materials and Methods
Microbiological, physicochemical, sensory evaluation, and volatile organic compounds (VOCs) analyses were conducted for samples of cooked rice stored at room temperature on days 0, 1, 2, and 3. SSO of cooked rice was then identified by linking present organisms with the changes occurring throughout the storage period.

Results
Microbiological analysis revealed the presence of spore-forming bacteria, yeast, and moulds, which survived the cooking process. While total viable count exceeded the microbiological limit at 6.90 log CFU/g on D3, panellists deemed cooked rice unacceptable for consumption on D2 at a total sensory score of 11.00, which indicates that D2 was the day cooked rice spoiled. Through culture-dependent and culture-independent methods, Bacillus cereus was identified as the sole bacteria observed throughout the storage period, confirming that the bacteria were SSOs. The VOC analysis proposed several metabolites, 3-eicosene, 1-heptadecene, hexacosane, phenol, 4,4ʹ-(1-methylethylidene)bis-, n-nonadecanol-1, and cyclohexanone, as potential spoilage markers of cooked rice.

Conclusions
B. cereus is confirmed to be the SSO of cooked rice, in which spoilage occured after 48 h of storage at room temperature. The organoleptic rejection in cooked rice was shown to be linked to the production of various compounds by B. cereus which could be proposed as potential spoilage markers for cooked rice.
What is a star worth to Medicare beneficiaries? A discrete choice experiment of hospital quality ratings
Authors: Trenaman Logan , Harrison Mark , Hoch Jeffrey S 
Published: December 2023

Abstract
Hospital quality ratings are widely available to help Medicare beneficiaries make an informed choice about where to receive care. However, how beneficiaries’ trade-off between different quality domains (clinical outcomes, patient experience, safety, efficiency) and other considerations (out-of-pocket cost, travel distance) is not well understood. We sought to study how beneficiaries make trade-offs when choosing a hypothetical hospital. We administered an online survey that included a discrete choice experiment to a nationally representative sample of 1025 Medicare beneficiaries. On average, beneficiaries were willing to pay $1698 more for a hospital with a 1-star higher rating on clinical outcomes. This was over twice the value of the patient experience ($691) and safety ($615) domains and nearly 8 times the value of the efficiency domain ($218). We also found that the value of a 1-star improvement depends not only on the quality domain but also the baseline level of performance of the hospital. Generally, it is more valuable for low-performing hospitals to achieve average performance than for average hospitals to achieve excellence.
An image of industry: exploring the effects of knowledge sources in the medical imaging industry
Authors: Park U David , Rha Youngsir , Shah Sonali K , Chattopadhyay Shinjinee 
Published: December 2023

Abstract
Scholars have long been interested in understanding how a firm’s “pre-history” shapes its behavior and performance, with recent scholarship highlighting the fact that industry entrants stem from different knowledge sources. Knowledge sources, the context in which entrants develop the knowledge they bring as they enter an industry, are argued to be important, because they may have differential effects on firm strategy and performance. We explore the effects of five different knowledge sources on firm behavior and survival using a mixed-methods approach. Survival analysis shows that user-founded new ventures outsurvive academic-founded new ventures, employee-founded new ventures, related diversifying entrants, and unrelated diversifying entrants. Qualitative analysis suggests that user-founded new ventures often enter niche markets defined by the clinical expertise of their founders and remain in these markets over time, honing their product offerings to specific clinical needs. Our analyses are based on novel, hand-collected archival data on the population of entrants in the modern medical imaging industry. We discuss the implications of these findings for the evolutionary theory, strategic management, and entrepreneurship literatures.
Employee spinouts along the value chain
Authors: Adams Pamela , Bahoo-Torodi Aliasghar , Fontana Roberto , Malerba Franco 
Published: December 2023

Abstract
While much of the academic literature on spinouts focuses on new ventures launched by the ex-employees of incumbent firms within the same industry, recent research shows that spinouts may also enter a focal industry from “knowledge contexts” outside of the incumbent industry. In particular, recent studies show that spinouts may enter from both upstream and downstream industries related to a focal industry along the value chain. Such spinouts have been called user-industry and supplier-industry spinouts. In this article, evidence from existing studies is collected to provide an indication of the relevance of such spinouts across various industries. This survey also includes an analysis of industry studies in which user- and supplier-industry spinouts may have been present but were not identified as such by scholars due to a difference in focus. The paper then considers the evidence accumulated to date in order to explore the industry contexts in which these two types of spinouts appear and to develop propositions concerning differences in the entry timing and product/market strategies of these startups.
Is a subxiphoid approach equivalent to midline sternotomy for extended thymectomy for achieving disease remission in patients with myasthenia gravis?
Authors: Zhu Alison , Kemp Ursula 
Published: December 2023

Summary
A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was ‘In patients with myasthenia gravis undergoing extended thymectomy, is a subxiphoid approach equivalent to midline sternotomy for achieving disease remission?’ Altogether 106 papers were found using the reported search, of which 5 represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. Five studies of a total of 803 patients with myasthenia gravis (MG) reported their experience with thymectomy by subxiphoid approach versus thymectomy by midline sternotomy. These studies demonstrated shorter operation duration, reduced intraoperative blood loss, reduced hospital length of stay and lower postoperative pain scores in the subxiphoid group. There was no significant difference in rates of postoperative MG crisis between the 2 groups, and similar rates of improvement in quantitative myasthenia gravis scores. We conclude that while further high-quality research is required, thymectomy by subxiphoid approach for MG may be considered in preference to midline sternotomy due to improved short-term postoperative outcomes and similar disease remission rates.
Playing a crop simulation model using symbols and sounds: the ‘mandala’
Authors: Bregaglio Simone , Carriero Giulia , Calone Roberta , Romano Maddalena , Bajocco Sofia 
Published: December 2023

Abstract
Abstract. Simulation models are primary tools for synthesizing plant physiological knowledge, supporting farmers’ decisions and predicting crop yields and functioning under climate change. The conventional approach within the scientific community consists of disseminating model outcomes through articles and technical reports, often impeding the share of knowledge among science, policy and society. This work presents the mandala (modelled and abstracted plant), a simulation model translating crop phenology and physiology as a function of environmental drivers into symbols and sounds, focussing on plant responses to cold, drought and heat stresses. The mandala has been realized with object-oriented (C#) and visual (vvvv) programming, and the source code is free for extension and improvement. We tested the mandala in six heterogeneous climates to show the potential to convey essential information on maize and wheat growth and responses to abiotic stresses. Despite lacking in artistic refinement, this work attempts to illustrate that visual and sound art can serve as unconventional means of disseminating crop model insights while showing their potential to enhance the breadth of information delivered to the public.