bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-time monitoring of process current and its correlation with micro-feature accuracy and surface topography in electrochemical micromachining of nitinol
Authors: Sethi Abhijeet , Acharya Biswesh Ranjan , Saha Partha 
Published: November 2023

Abstract
The nickel-titanium alloy known as Nitinol classified as a shape memory alloy is distinguished by its exceptional attributes, including shape memory effect, biocompatibility, and superelasticity. However, its thermo-mechanical dependent transformation behavior makes it difficult to process using traditional methods. Electrochemical micromachining (ECMM), a non-traditional fabrication method, uses anodic dissolution process to produce microfeatures on Nitinol. The current work emphasizes the impact of process current on the machining accuracy and surface topography of microchannels produced during ECMM of Nitinol utilizing ethylene glycol-based sodium nitrate electrolyte. The ECMM process parameters that were studied are pulsed potential, molar concentration, and micro-tool scan rate, and the development of the process current resulting in variation of these parameters during microchannel fabrication was closely observed. The statistical parameters, namely, the average process current and the process current fluctuation, were derived from the process current data that were further analyzed with respect to input parameters. The machining accuracy and the surface topography of the microchannel are analyzed by measuring the width overcut, channel depth, stray region, width standard deviation, and average surface roughness of the fabricated microchannel. The results showed that monitoring the process current in real-time is an effective way of controlling the process, particularly when it comes to fabricating micro-features that must adhere to strict predetermined criteria.
Procyanidins and sensory nutrition; do procyanidins modulate homeostasis via astringent taste receptors?
Authors: Osakabe Naomi , Fushimi Taiki , Fujii Yasuyuki , Calabrese Vittorio 
Published: November 2023

ABSTRACT
Long-term intake of procyanidins has been suggested to reduce the risk of cardiovascular disease, dementia, and sensory function decline associated with aging. However, most of the ingested procyanidins are not absorbed and are excreted in the feces, so the mechanism of their beneficial impact is unknown. Procyanidins are the components of astringency in plant foods and their stimulation appears to be directly transmitted to the central nervous system via sensory nerves. Recent attention has been focused on the taste receptors expressed in the extra-oral gastrointestinal tract may regulate homeostasis via the neuroendocrine system. In this paper, we have reviewed recent findings on the relationship between the astringency of procyanidins and their bioregulatory effects.
Housework or vigilance? Bilbies alter their burrowing activity under threat of predation by feral cats
Authors: Chen Faith S E , Dawson Stuart J , Fleming Patricia A 
Published: November 2023

Abstract
Behavioral adjustments to predation risk not only impose costs on prey species themselves but can also have cascading impacts on whole ecosystems. The greater bilby (Macrotis lagotis) is an important ecosystem engineer, modifying the physical environment through their digging activity, and supporting a diverse range of sympatric species that use its burrows for refuge and food resources. The bilby has experienced a severe decline over the last 200 years, and the species is now restricted to ~20% of its former distribution. Introduced predators, such as the feral cat (Felis catus), have contributed to this decline. We used camera traps to monitor bilby burrows at four sites in Western Australia, where bilbies were exposed to varying levels of cat predation threat. We investigated the impact of feral cats on bilby behavior at burrows, particularly during highly vulnerable periods when they dig and clear away soil or debris from the burrow entrance as they perform burrow maintenance. There was little evidence that bilbies avoided burrows that were visited by a feral cat; however, bilbies reduced the time spent performing burrow maintenance in the days following a cat visit (P = 0.010). We found the risk posed to bilbies varied over time, with twice the cat activity around full moon compared with dark nights. Given bilby burrows are an important resource in Australian ecosystems, predation by feral cats and the indirect impact of cats on bilby behavior may have substantial ecosystem function implications.
ComplexQA: a deep graph learning approach for protein complex structure assessment
Authors: Zhang Lei , Wang Sheng , Hou Jie , Si Dong , Zhu Junyong , Cao Renzhi 
Published: November 2023

Abstract

Motivation
In recent years, the end-to-end deep learning method for single-chain protein structure prediction has achieved high accuracy. For example, the state-of-the-art method AlphaFold, developed by Google, has largely increased the accuracy of protein structure predictions to near experimental accuracy in some of the cases. At the same time, there are few methods that can evaluate the quality of protein complexes at the residue level. In particular, evaluating the quality of residues at the interface of protein complexes can lead to a wide range of applications, such as protein function analysis and drug design. In this paper, we introduce a new deep graph neural network-based method ComplexQA, to evaluate the local quality of interfaces for protein complexes by utilizing the residue-level structural information in 3D space and the sequence-level constraints.

Results
We benchmark our method to other state-of-the-art quality assessment approaches on the HAF2 and DBM55-AF2 datasets (high-quality structural models predicted by AlphaFold-Multimer), and the BM5 docking dataset. The experimental results show that our proposed method achieves better or similar performance compared with other state-of-the-art methods, especially on difficult targets which only contain a few acceptable models. Our method is able to suggest a score for each interfac e residue, which demonstrates a powerful assessment tool for the ever-increasing number of protein complexes.

Availability
https://github.com/Cao-Labs/ComplexQA.git. Contact: caora@plu.edu
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval
Authors: Jin Qiao , Kim Won , Chen Qingyu , Comeau Donald C , Yeganova Lana , Wilbur W John , Lu Zhiyong 
Published: November 2023

Abstract

Motivation
Information retrieval (IR) is essential in biomedical knowledge acquisition and clinical decision support. While recent progress has shown that language model encoders perform better semantic retrieval, training such models requires abundant query–article annotations that are difficult to obtain in biomedicine. As a result, most biomedical IR systems only conduct lexical matching. In response, we introduce MedCPT, a first-of-its-kind Contrastively Pre-trained Transformer model for zero-shot semantic IR in biomedicine.

Results
To train MedCPT, we collected an unprecedented scale of 255 million user click logs from PubMed. With such data, we use contrastive learning to train a pair of closely integrated retriever and re-ranker. Experimental results show that MedCPT sets new state-of-the-art performance on six biomedical IR tasks, outperforming various baselines including much larger models, such as GPT-3-sized cpt-text-XL. In addition, MedCPT also generates better biomedical article and sentence representations for semantic evaluations. As such, MedCPT can be readily applied to various real-world biomedical IR tasks.

Availability and implementation
The MedCPT code and model are available at https://github.com/ncbi/MedCPT.
Discontinuation of anti-tumour necrosis factor alpha treatment owing to blood test abnormalities, and cost-effectiveness of alternate blood monitoring strategies
Authors: Abhishek Abhishek , Stevenson Matthew D , Nakafero Georgina , Grainge Matthew J , Evans Ian , Alabas Oras , Card Tim , Taal Maarten W , Aithal Guruprasad P , Fox Christopher P , Mallen Christian D , van der Windt Danielle A , Riley Richard D , Warren Richard B , Williams Hywel C 
Published: November 2023

Abstract

Background
There is no evidence base to support the use of 6-monthly monitoring blood tests for the early detection of liver, blood and renal toxicity during established anti-tumour necrosis factor alpha (TNFα) treatment.

Objectives
To evaluate the incidence and risk factors of anti-TNFα treatment cessation owing to liver, blood and renal side-effects, and to estimate the cost-effectiveness of alternate intervals between monitoring blood tests.

Methods
A secondary care-based retrospective cohort study was performed. Data from the British Association of Dermatologists Biologic and Immunomodulators Register (BADBIR) were used. Patients with at least moderate psoriasis prescribed their first anti-TNFα treatment were included. Treatment discontinuation due to a monitoring blood test abnormality was the primary outcome. Patients were followed-up from start of treatment to the outcome of interest, drug discontinuation, death, 31 July 2021 or up to 5 years, whichever came first. The incidence rate (IR) and 95% confidence intervals (CIs) of anti-TNFα discontinuation with monitoring blood test abnormality was calculated. Multivariate Cox regression was used to examine the association between risk factors and outcome. A mathematical model evaluated costs and quality-adjusted life years (QALYs) associated with increasing the length of time between monitoring blood tests during anti-TNFα treatment.

Results
The cohort included 8819 participants [3710 (42.1%) female, mean (SD) age 44.76 (13.20) years] that contributed 25 058 person-years (PY) of follow-up and experienced 125 treatment discontinuations owing to a monitoring blood test abnormality at an IR of 5.85 (95% CI 4.91–6.97)/1000 PY. Of these, 64 and 61 discontinuations occurred within the first year and after the first year of treatment start, at IRs of 8.62 (95% CI 6.74–11.01) and 3.44 (95% CI 2.67–4.42)/1000 PY, respectively. Increasing age (in years), diabetes and liver disease were associated with anti-TNFα discontinuation after a monitoring blood test abnormality [adjusted hazard ratios of 1.02 (95% CI 1.01–1.04), 1.68 (95% CI 1.00–2.81) and 2.27 (95% CI 1.26–4.07), respectively]. Assuming a threshold of £20 000 per QALY gained, no monitoring was most cost-effective, but all extended periods were cost-effective vs. 3- or 6-monthly monitoring.

Conclusions
Anti-TNFα drugs were uncommonly discontinued owing to abnormal monitoring blood tests after the first year of treatment. Extending the duration between monitoring blood tests was cost-effective. Our results produce evidence for specialist society guidance to reduce patient monitoring burden and healthcare costs.
Expectation Formation with Correlated Variables
Authors: He Simin , Kučinskas Simas 
Published: November 2023

Abstract
We experimentally study how people form expectations about correlated variables. Subjects forecast a time-series variable A. In treatment Baseline, subjects only observe past values of A. In treatment Correlated, they additionally observe a correlated variable B; A is equally predictable and has the same univariate properties in both treatments. Subjects are significantly less accurate and underreact more in Correlated, inconsistent with Bayesian learning. A structural-model estimation indicates that subjects (i) underestimate the level of correlation and (ii) are insensitive to actual correlation. Our study provides first direct evidence of correlation neglect in the domain of expectation formation.
Frozen elephant trunk technique using hybrid grafts: 15-year outcomes from a single-centre experience
Authors: Murana Giacomo , Gliozzi Gregorio , Di Marco Luca , Campanini Francesco , Snaidero Silvia , Nocera Chiara , Rucci Paola , Barberio Giuseppe , Leone Alessandro , Lovato Luigi , Pacini Davide 
Published: November 2023

Abstract

OBJECTIVES
The purpose of the study is to compare the short- and long-term outcomes of the frozen elephant trunk (FET) technique based on 2 different hybrid grafts implanted from January 2007 to July 2022.

METHODS
The study includes patients who underwent an elective or emergency FET procedure. Short-term, long-term mortality and freedom from thoracic endovascular aortic repair (TEVAR) were the primary end points. Analyses were carried out separately for the periods 2007–2012 and 2013–2022

RESULTS
Of the 367 enrolled, 49.3% received E-Vita Open implantation and 50.7% received Thoraflex Hybrid implants. Overall mean age was 61 years [standard deviation (SD) = 11] and 80.7% were male. The average annual volume of FET procedures was 22.7 cases/year. Compared to E-Vita Open, patients implanted with Thoraflex Hybrid grafts were more likely to receive distal anastomosis in zone 2 (68.3% vs 11.6%, P &lt; 0.001) with a shorter stent portion, mean = 103mm (SD = 11.3) vs mean = 149 mm (SD = 12.7; P &lt; 0.001) and they underwent a reduced visceral ischaemia time, mean = 42.5 (SD = 14.2) vs mean= 61.0 (SD = 20.2) min, P &lt; 0.001. In the period 2013–2022, overall survival at 1, 2 and 5 years was 74.8%, 72.5% and 63.2% for Thoraflex and 73.2%, 70.7% and 64.1% for E-Vita, without significant differences between groups (log-rank test = 0.01, P = 0.907). Overall freedom from TEVAR at 1, 2 and 5 years was 66.7%, 57.6% and 39.3% for Thoraflex and 79%, 69.7% and 66% for E-Vita, with significant differences between groups (log-rank test = 5.28, P = 0.029). In a competing risk analysis adjusted for chronic/residual aortic syndromes and stent diameter, the Thoraflex group was more likely to receive TEVAR during follow-up (subdistribution hazard ratio SHR = 2.12, 95% confidence interval 1.06–4.22).

CONCLUSIONS
The FET technique addresses acute and chronic arch disease with acceptable morbidity and mortality. Downstream endovascular reinterventions are very common during follow-up.
Risk factors for loss of pulmonary function after wedge resection for peripheral ground-glass opacity dominant lung cancer
Authors: Miyoshi Tomohiro , Ito Hiroyuki , Wakabayashi Masashi , Hashimoto Tadayoshi , Sekino Yuta , Suzuki Kenji , Tsuboi Masahiro , Moriya Yasumitsu , Yoshino Ichiro , Isaka Tetsuya , Hattori Aritoshi , Mimae Takahiro , Isaka Mitsuhiro , Maniwa Tomohiro , Endo Makoto , Yoshioka Hiroshige , Nakagawa Kazuo , Nakajima Ryu , Tsutani Yasuhiro , Saji Hisashi , Okada Morihito , Aokage Keiju , Fukuda Haruhiko , Watanabe Shun-Ichi 
Published: November 2023

Abstract

OBJECTIVES
This study aimed to identify the risk factors for pulmonary functional deterioration after wedge resection for early-stage lung cancer with ground-glass opacity, which remain unclear, particularly in low-risk patients.

METHODS
We analysed 237 patients who underwent wedge resection for peripheral early-stage lung cancer in JCOG0804/WJOG4507L, a phase III, single-arm confirmatory trial. The changes in forced expiratory volume in 1 s were calculated pre- and postoperatively, and a cutoff value of −10%, the previously reported reduction rate after lobectomy, was used to divide the patients into 2 groups: the severely reduced group (≤−10%) and normal group (&gt;−10%). These groups were compared to identify predictors for severe reduction.

RESULTS
Thirty-seven (16%) patients experienced severe reduction. Lesions with a total tumour size ≥1 cm were significantly more frequent in the severely reduced group than in the normal group (89.2% vs 71.5%; P = 0.024). A total tumour size of ≥1 cm [odds ratio (OR), 3.287; 95% confidence interval (CI), 1.114–9.699: P = 0.031] and pleural indentation (OR, 2.474; 95% CI, 1.039–5.890: P = 0.041) were significant predictive factors in the univariable analysis. In the multivariable analysis, pleural indentation (OR, 2.667; 95% CI, 1.082–6.574; P = 0.033) was an independent predictive factor, whereas smoking status and total tumour size were marginally significant.

CONCLUSIONS
Of the low-risk patients who underwent pulmonary wedge resection for early-stage lung cancer, 16% experienced severe reduction in pulmonary function. Pleural indentation may be a risk factor for severely reduced pulmonary function in pulmonary wedge resection.
All about being old and shooting hairs: clade age and urticating hair explain the patterns of diversification in tarantulas
Authors: Biswas Aritra , Karanth K Praveen 
Published: November 2023

Abstract
The extreme asymmetry of species richness distribution across the tree of life has always intrigued evolutionary biologists. Two competing explanations have been proposed to explain this pattern—the clade age hypothesis and diversification rate variation. While these two scenarios may not be mutually exclusive, to what extent time and diversification rates interact to explain species richness patterns remains understudied. Here, we investigate the relative influence of these two scenarios using tarantulas (Family: Theraphosidae) as a model. Tarantulas represent a speciose group of spiders found worldwide but exceptionally diverse in South America. These spiders show two distinct patterns of microhabitat use (ground-dwelling or arboreal) and defense strategies (presence or absence of urticating hairs). Using various trait-independent and dependent diversification models, we test the clade age hypothesis, the role of microhabitat, antipredator defense strategy, and geography in influencing diversification rates. Our results suggest that clade age is the primary predictor of species richness distribution across the tarantula subfamilies. However, the presence of urticating hair probably disrupted this pattern in some clades by increasing the net diversification rates, not by increasing the speciation rate but by reducing the extinction rate.
Three-dimensional electric-field vector resistivity imaging for deep subsurface fractures network in heterogeneous crystalline rocks
Authors: Maurya V P , Gupta S M , Mishra A , Chandra S , Tiwari V M 
Published: November 2023

SUMMARY
Crystalline rocks, exposed in different parts of the world and over about one-third of India, have complex aquifer systems, which pose a challenge to mapping groundwater dynamics. Electrical resistivity tomography in quasi-3-D and electrical logging of some borewells carried out in an experimental ‘hydrogeological park’ in southern India, which has numerous boreholes and other geophysical information for validation, were unable to map the existence of deeper bedrock fractures and their connectivity. We have attempted electric-field vector resistivity imaging (EVRI), a new tool, to resolve the possible fracture-induced deep interconnectivity in a hard rock aquifer system. In the experiment, multiple two-orthonormal-channels independent receiver nodes for potential measurements are deployed and illuminated with several current injections between ∼ 0.9–3.7 A in full 3-D fashion, which allowed for improved mapping of resistivity variation than earlier approaches. The EVRI-derived full 3-D model shows the presence of fractures for depths between 20 and 70 m with substantial resistivity variations, supported by some borewells hydraulic investigations. It has also enhanced lateral resolution for depths &gt; 30 m and almost doubled the depth of investigation than earlier electrical models. EVRI results revealed unweathered/unfractured granitic rock with no significant signature of fractures beyond 70 m depth that corroborates with existing borehole logs and hydrogeological conceptual model. Therefore, this study demonstrates the potential of EVRI for 3-D mapping of heterogeneous crystalline rocks, which would greatly help in groundwater management.
Ralph of Diss, the coronation of Philip Augustus (1179) and the English claim to the French throne
Authors: Weiler Björn 
Published: November 2023

Abstract
In the 1190s Ralph of Diss, the dean of St. Paul’s Cathedral, London, wrote a universal chronicle from the Creation to the author’s lifetime. This article uses Ralph’s account of the coronation of Philip Augustus of France in 1179 to tackle a series of broader issues: the role of history as a form of erudition, the ability of a remote and distant past to contain lessons for the present, and how this may change our approach to the works of Diss and his brethren. This represents the first attempt to read Ralph’s writings taking seriously his instructions about how history ought to be approached. The interpretation of events in 1179 casts important new light on Ralph’s approach to history, as well as on elite literary and historical culture around the year 1200.
Three linked variants have opposing regulatory effects on isovaleryl-CoA dehydrogenase gene expression
Authors: Brown Elizabeth A , Kales Susan , Boyle Michael James , Vitti Joseph , Kotliar Dylan , Schaffner Steve , Tewhey Ryan , Sabeti Pardis C 
Published: November 2023

Abstract
While genome-wide association studies (GWAS) and positive selection scans identify genomic loci driving human phenotypic diversity, functional validation is required to discover the variant(s) responsible. We dissected the IVD gene locus—which encodes the isovaleryl-CoA dehydrogenase enzyme—implicated by selection statistics, multiple GWAS, and clinical genetics as important to function and fitness. We combined luciferase assays, CRISPR/Cas9 genome-editing, massively parallel reporter assays (MPRA), and a deletion tiling MPRA strategy across regulatory loci. We identified three regulatory variants, including an indel, that may underpin GWAS signals for pulmonary fibrosis and testosterone, and that are linked on a positively selected haplotype in the Japanese population. These regulatory variants exhibit synergistic and opposing effects on IVD expression experimentally. Alleles at these variants lie on a haplotype tagged by the variant most strongly associated with IVD expression and metabolites, but with no functional evidence itself. This work demonstrates how comprehensive functional investigation and multiple technologies are needed to discover the true genetic drivers of phenotypic diversity.
DC-targeting lentivectors for cancer immunotherapy
Authors: Gea-Mallorquí Ester , Rowland-Jones Sarah 
Published: November 2023

Summary
Lentivectors (LVs) induce sustained transgene expression and are attractive vaccine platforms for complex immune scenarios like cancer and persistent infections. This review summarises the literature on lentivectors with potential uses for in vivo immunotherapy, focussing on those targeting the most potent antigen-presenting cells: dendritic cells (DCs). There is a growing interest in myeloid-targeting therapies as, by influencing an early stage in the immune hierarchy, they can orchestrate a more diverse and complex targeted immune response. We dissect the nature of DC-targeting LVs and their induced immune responses to understand the state of the art, identify the knowledge gaps and guide efforts to maximise the generation of potent and effective immune responses. Lentivector-based vaccines provide several advantages over other vaccine platforms, such as directed tropism and limited vector immunogenicity, and have been shown to generate effective and sustained immune responses. Overall, DC-targeting lentivectors stand out as promising tools to be exploited in cancer immunotherapy, and new-generation LVs can further exploit the gained knowledge in the study of naturally occurring lentiviruses for a more directed and adjuvanted response.