bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of tool geometry on ultraprecision machining of soft-brittle materials: a comprehensive review
Authors: Huang Weihai , Yan Jiwang 
Published: December 2022

Abstract
Brittle materials are widely used for producing important components in the industry of optics, optoelectronics, and semiconductors. Ultraprecision machining of brittle materials with high surface quality and surface integrity helps improve the functional performance and lifespan of the components. According to their hardness, brittle materials can be roughly divided into hard-brittle and soft-brittle. Although there have been some literature reviews for ultraprecision machining of hard-brittle materials, up to date, very few review papers are available that focus on the processing of soft-brittle materials. Due to the ‘soft’ and ‘brittle’ properties, this group of materials has unique machining characteristics. This paper presents a comprehensive overview of recent advances in ultraprecision machining of soft-brittle materials. Critical aspects of machining mechanisms, such as chip formation, surface topography, and subsurface damage for different machining methods, including diamond turning, micro end milling, ultraprecision grinding, and micro/nano burnishing, are compared in terms of tool-workpiece interaction. The effects of tool geometries on the machining characteristics of soft-brittle materials are systematically analyzed, and dominating factors are sorted out. Problems and challenges in the engineering applications are identified, and solutions/guidelines for future R&D are provided.
Musical Silences—Opaque and Capacious
Authors: Hulatt Owen 
Published: December 2022

Abstract
I will argue that there are (at least) two species of musical silence, which cannot be distinguished by attending to how these silences sound. I term these two kinds of musical silence ‘capacious’ and ‘opaque’. Both capacious and opaque musical silences might occur in the midst of the ongoing production of sound or might exist in the complete absence of sound. Both kinds of silence can, in certain conditions, be sonically identical, but both are always received by the listening ear in importantly different ways. I will discuss our ability to distinguish between these silences, even when they ‘sound’ the same. I will argue that the accounts of musical silence and silent music offered by (among others) Levinson, Kania, and Davies are vitiated by their failure to distinguish between these kinds of musical silence. I distinguish these kinds of silence by the kinds of listening activity associated with them, and the ideal structure of such listening practices.
DPADM: a novel algorithm for detecting drug-pathway associations based on high-throughput transcriptional response to compounds
Authors: Wang Yishu , Qi Juan , Ai Dongmei 
Published: December 2022

AbstractPathway genes functionally participate in the same biological process. They typically act cooperatively, and none is considered dispensable. The dominant paradigm in drug discovery is the one-to-one strategy, which aims to find the most sensitive drug to act on an individual target. However, many complex diseases, such as cancer, are caused by dysfunction among multiple-gene pathways, not just one. Therefore, identifying pathway genes that are responsive to synthetic compounds in a global physiological environment may be more effective in drug discovery. The high redundancy of crosstalk between biological pathways, though, hints that the covariance matrix, which only connects genes with strong marginal correlations, may miss higher-level interactions, such as group interactions. We herein report the development of DPADM—a Drug-Pathway association Detection Model that infers pathways responsive to specific drugs. This model elucidates higher-level gene–gene interactions by evaluating the conditional dependencies between genes under different drug treatments. The advantage of the proposed method is demonstrated using simulation studies by comparing with another two methods. We applied this model to the Connectivity Map data set (CMap), and demonstrated that DPADM is able to identify many drug-pathway associations, such as mitoxantrone (MTX)- PI3K/AKT association, which targets the topological conditions of DNA transcription. Surprisingly, apart from identifying pathways corresponding to specific drugs, our methodology also revealed new drug-related pathways with functions similarly to those of seed genes.
CRMSS: predicting circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features
Authors: Zhang Lishen , Lu Chengqian , Zeng Min , Li Yaohang , Wang Jianxin 
Published: December 2022

Abstract
Circular RNAs (circRNAs) are reverse-spliced and covalently closed RNAs. Their interactions with RNA-binding proteins (RBPs) have multiple effects on the progress of many diseases. Some computational methods are proposed to identify RBP binding sites on circRNAs but suffer from insufficient accuracy, robustness and explanation. In this study, we first take the characteristics of both RNA and RBP into consideration. We propose a method for discriminating circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features, called CRMSS. For circRNAs, we use sequence ${k}\hbox{-}{mer}$ embedding and the forming probabilities of local secondary structures as features. For RBPs, we combine sequence and structure frequencies of RNA-binding domain regions to generate features. We capture binding patterns with multi-scale residual blocks. With BiLSTM and attention mechanism, we obtain the contextual information of high-level representation for circRNA-RBP binding. To validate the effectiveness of CRMSS, we compare its predictive performance with other methods on 37 RBPs. Taking the properties of both circRNAs and RBPs into account, CRMSS achieves superior performance over state-of-the-art methods. In the case study, our model provides reliable predictions and correctly identifies experimentally verified circRNA-RBP pairs. The code of CRMSS is freely available at https://github.com/BioinformaticsCSU/CRMSS.
Human Immunodeficiency Virus Is Associated With Poor Overall Survival Among Patients With Head and Neck Cancer
Authors: Salahuddin Syim , Cohen Oded , Wu Margaret , Perez Irizarry Javier , Vega Teresita , Gan Geliang , Deng Yanhong , Isaeva Natalia , Prasad Manju , Schalper Kurt A , Mehra Saral , Yarbrough Wendell G , Emu Brinda 
Published: December 2022

AbstractBackgroundHead and neck squamous cell cancer (HNSCC) occurs at higher rates among persons with HIV (PWH). This study compares the impact of sociodemographic and clinicopathologic characteristics on outcomes among PWH-HNSCC compared with HNSCC patients without HIV.MethodsPatient data from HNSCC individuals were collected at a single academic hospital center between 2002 and 2018. Forty-eight patients with HIV (HIV-HNSCC) and 2894 HNSCC patients without HIV were included. Multivariate analysis determined predictors of survival using Cox proportional hazards regression model. HIV-positive and -negative tumors were analyzed by quantitative immunofluorescence for expression of CD4, CD8, CD20 and PD-L1.ResultsHIV-HNSCC patients had a lower median overall survival than HNSCC patients without HIV (34 [18–84] vs 94 [86–103] months; P &lt; .001). In multivariate analysis that included age, sex, race/ethnicity, stage, site, tobacco use, time to treatment initiation, and insurance status, HIV was an independent predictor of poorer survival, with a hazard ratio of 1.98 (95% CI: 1.32–2.97; P &lt; .001). PWH with human papillomavirus (HPV)–positive oropharyngeal tumors also had worse prognosis than HPV-positive oropharyngeal tumors in the population without HIV (P &lt; .001). The tumor microenvironment among HIV-HNSCC patients revealed lower intratumoral CD8 infiltration among HIV+ HPV+ tumors compared with HIV– HPV+ tumors (P = .04).ConclusionsHIV-HNSCC patients had worse prognosis than the non-HIV population, with HIV being an independent predictor of poor clinical outcomes when accounting for important sociodemographic and clinicopathologic factors. Our findings highlight differences in tumor biology that require further detailed characterization in large cohorts and increased inclusion of PWH in immunotherapy trials.
Risk Factors and Outcomes of Invasive Aspergillosis in Kidney Transplant Recipients: A Case-Control Study of United States Renal Data System Data
Authors: Friedman Daniel Z P , Johnson Bradley K , Beam Elena , Kremers Walter K , Vergidis Paschalis 
Published: December 2022

AbstractBackgroundKidney transplant recipients are at increased risk for invasive aspergillosis (IA), a disease with poor outcomes and substantial economic burden. We aimed to determine risk factors for posttransplant IA by using a national database and to assess the association of IA with mortality and allograft failure.MethodsUsing the United States Renal Data System database, we performed a retrospective case-control study of patients who underwent kidney transplant from 1998 through 2017. To evaluate risk factors for IA, we performed conditional logistic regression analysis by comparing characteristics between IA-infected patients and their matched uninfected controls. We performed Cox regression analysis to evaluate the effects of IA on mortality and death-censored allograft failure.ResultsWe matched 359 patients with IA to 1436 uninfected controls (1:4). IA was diagnosed at a median of 22.5 months (interquartile range, 5.4–85.2 months) after kidney transplant. Risk factors for IA were Black/African American race, duration of pretransplant hemodialysis, higher Elixhauser Comorbidity Index score, weight loss, chronic pulmonary disease, need for early posttransplant hemodialysis, and a history of cytomegalovirus infection. Receiving an allograft from a living donor was protective against IA. IA was a strong independent predictor of 1-year mortality (adjusted hazard ratio [aHR], 5.02 [95% confidence interval {CI}, 3.58–7.04], P &lt; .001). Additionally, IA was associated with 1-year allograft failure (aHR, 3.37 [95% CI, 1.96–5.77], P &lt; .001).ConclusionsOur findings emphasize the importance of timely transplant to mitigate the risk of posttransplant IA. An individualized approach to disease prevention is essential to decrease mortality and allograft failure.
What advice do general practitioners give to people living with obesity to lose weight? A qualitative content analysis of recorded interactions
Authors: Tremblett Madeleine , Poon Annabel Y X , Aveyard Paul , Albury Charlotte 
Published: December 2022

Abstract

Background
Guidelines recommend general practitioners (GPs) take every opportunity to talk to people living with obesity about their weight, and evidence shows even very brief advice is associated with weight loss. However, little is known about what GPs say when giving brief behavioural advice, and if it reflects evidence-based recommendations for people living with obesity. To understand what behavioural advice GPs give, we categorized the content and delivery of GPs’ advice during brief interventions.

Methods
Qualitative content analysis was applied to 159 audio recordings of consultations from the Brief Interventions for Weight Loss (BWeL) trial, where GPs gave brief weight-loss advice to patients with a body mass index ≥30 kg/m2 (or ≥25 kg/m2 if Asian) in 137 UK surgeries. Similar content was grouped into descriptive clusters.

Results
The results comprised 4 clusters, illuminating different aspects of the advice given: (i) Content of diet and physical activity advice, showing this was highly varied; (ii) Content of “implementation tips” given to support changes, e.g. using smaller plates; (iii) Content of signposting support, either towards further clinician support, or other resources, e.g. information booklets; (iv) Style of advice delivery, showing GPs rarely gave personalized advice, or reasons for their advice.

Conclusions and implications
Weight-loss advice from GPs to patients with obesity rarely included effective methods, mostly communicating a general “eat less, do more” approach. Advice was mostly generic, and rarely tailored to patients’ existing knowledge and behaviours. Effectiveness of brief weight-loss advice could be improved if GPs were given clearer guidance on evidence-based recommendations.
Brain Proteome-Wide and Transcriptome-Wide Asso-ciation Studies, Bayesian Colocalization, and Mendelian Randomization Analyses Reveal Causal Genes of Parkinson’s Disease
Authors: Zhou Siquan , Tian Ye , Song Xuejiao , Xiong Jingyuan , Cheng Guo 
Published: December 2022

AbstractHow genome-wide associated loci confer risk for Parkinson’s disease is unclear. We aim to reveal causal genes through effects on brain proteins to provide new pathogenesis insights for Parkinson’s disease. Proteome-wide and transcriptome-wide associations were determined by functional summary-based imputation leveraging data from genome-wide association summary (56 306 Europeans, 1.4 million controls), brain proteomes (528 cases from 2 separate data sets), and transcriptome (452 cases), followed by Mendelian randomization, Bayesian colocalization, cell-type-specific and brain regional expression, and drug–gene interaction analyses. As a result, genetically regulated protein abundances of 11 genes were associated with Parkinson’s disease. Five genes (CD38, GPNMB, TMEM175, RAB7L1, and HIP1R) were colocalized. Four genes (GPNMB, SEC23IP, CD38, and DGKQ) demonstrated Mendelian randomized correlations (p &lt; 8.10 × 10−5). Higher GPNMB level (1.47, 1.28–1.68) and lower CD38 level (0.319, 0.24–0.43) were causally associated with higher risk of Parkinson’s disease, consistent with transcriptomic evaluations. CD38 and GPNMB were preferentially enriched in astrocytes and oligodendrocyte precursor cells, respectively. And CD38 and GPNMB were suggested to be the targets of many oncological drugs from Drug–Gene Interaction database. In conclusion, utilizing multidimensional data, GPNMB and CD38 were prioritized as the causal genes of Parkinson’s disease, crucial for mechanistic and therapeutic investigations.
The Aging–Cancer Cycle: Mechanisms and Opportunities for Intervention
Authors: Sedrak Mina S , Cohen Harvey Jay 
Published: December 2022

Abstract
Aging is the largest risk factor for the development of cancer. A growing body of literature indicates that aging and cancer often play a somewhat reciprocal relationship at various times. On the one hand, aging is a “driver” of cancer, and on the other, cancer is a “disease driver” of aging. Here, we synthesize our reflections on the current literature linking cancer and aging, with an eye on fundamental aging processes, such as cellular senescence. Additionally, we consider how interventions that target fundamental aging processes can potentially transform cancer care, from preventing cancer development and progression to reducing the burden of accelerated aging in cancer survivors. Finally, we conclude with a reflection highlighting our vision for future directions to advance the science of cancer and aging and its applicability to improve the care of older adults with cancer.
Upregulation of non-canonical and canonical inflammasome genes associates with pathological features in Krabbe disease and related disorders
Authors: Cachón-González María B , Zhao Chao , Franklin Robin J , Cox Timothy M 
Published: December 2022

AbstractInfantile Krabbe disease is a rapidly progressive and fatal disorder of myelin, caused by inherited deficiency of the lysosomal enzyme β-galactocerebrosidase. Affected children lose their motor skills and other faculties; uncontrolled seizures are a frequent terminal event. Overexpression of the sphingolipid metabolite psychosine is a pathogenic factor, but does not fully account for the pleiotropic manifestations and there is a clear need to investigate additional pathological mechanisms. We examined innate immunity, caspase-11 and associated inflammatory pathways in twitcher mice, an authentic model of Krabbe disease. Combined use of molecular tools, RNAscope in situ hybridization and immunohistochemical staining established that the expression of pro-inflammatory non-canonical caspase-11, canonical caspase-1, gasdermin D and cognate genes is induced in nervous tissue. Early onset and progressive upregulation of these genes accompany demyelination and gliosis and although the molecules are scant in healthy tissue, abundance of the respective translation products is greatly increased in diseased animals. Caspase-11 is found in reactive microglia/macrophages as well as astrocytes but caspase-1 and gasdermin D are restricted to reactive microglia/macrophages. The inflammasome signature is not unique to Krabbe disease; to varying degrees, this signature is also prominent in other lysosomal diseases, Sandhoff and Niemann-Pick Type-C1, and the lysolecithin toxin model of focal demyelination. Given the potent inflammatory response here identified in Krabbe disease and the other neurodegenerative disorders studied, a broad induction of inflammasomes is likely to be a dominant factor in the pathogenesis, and thus represents a platform for therapeutic exploration.
Oral Health and Social Work Integration: Advancing Social Workers’ Roles in Dental Education
Authors: Zerden Lisa de Saxe , Morris Melanie , Burgess-Flowers Jamie 
Published: December 2022

AbstractOral health remains underutilized within both integrated service delivery and educational settings. Advancing social workers’ roles in the education of oral health providers is one strategic way to expand oral health and social work integration. Although the involvement of social workers in dental education is not new, fewer than 18 percent of the country’s 68 accredited dental schools have active social work departments or services. This exploratory study sought to determine how, as of 2021, social work has been integrated into U.S. dental education programs (N = 13). Findings offer an overview of current social work programs in existence, roles social workers have in addressing social and behavioral health needs in dental education settings, and barriers to and facilitators in developing and sustaining integrated partnerships. This article discusses ways social work and oral health educational settings can mutually benefit from developing and/or strengthening their integrated collaborations. It also addresses a comparison of educational missions, clinical learning opportunities across both professions, and how patient care can be improved by expanding oral health and social work integration.
Predicting bycatch of Chinook salmon in the Pacific hake fishery using spatiotemporal models
Authors: Shirk Philip L , Richerson Kate , Banks Michael , Tuttle Vanessa 
Published: December 2022

AbstractFisheries bycatch is a global problem, and the ability to avoid incidental catch of non-target species is important to fishermen, managers, and conservationists. In areas with sufficient data, spatiotemporal models have been used to identify times and locations with high bycatch risk, potentially enabling fishing operations to shift their effort in response to the dynamic ocean landscape. Here, we use 18 years of observer data from the Pacific hake (Merluccius productus) fishery, the largest by tonnage on the US West Coast, to evaluate our ability to predict bycatch of the commercially, culturally, and ecologically important Chinook salmon (Oncorhynchus tshawytscha). Using multiple approaches (regression models, tree-based methods, and model averages), we tested our ability to predict bycatch at weekly and yearly timescales and found that spatiotemporal models can have good predictive ability. Gradient boosting trees (GBTs) and model averages typically had higher performance, while generalized linear models and generalized additive models (without interaction terms) did less well. Using a GBT model to remove 1% of hauls with the highest predicted bycatch reduced the bycatch-to-hake ratio by 20%. Our results indicate that spatiotemporal models may be a useful forecasting tool that can help fishing operations avoid bycatch while minimizing losses from target catches.
Bilinear Fourier Multipliers of Bounded Variation
Authors: Baena-Miret Sergi , Carro María J , Luque Teresa , Sánchez-Pascuala Laura 
Published: December 2022

Abstract
In this paper, we obtain weighted estimates for bilinear Fourier multipliers of bounded variation that provide new restricted weak-type bounds. We also study their boundedness on the setting of the weighted Lorentz spaces. The results are obtained using Rubio de Francia extrapolation as the main tool.
Structural equation modelling the impact of antimicrobials on the human microbiome. Colonization resistance versus colonization susceptibility as case studies
Authors: Hurley James C 
Published: December 2022

AbstractThe impact of antimicrobials on the human microbiome and its relationship to human health are of great interest. How antimicrobial exposure might drive change within specific constituents of the microbiome to effect clinically relevant endpoints is difficult to study. Clinical investigation of each step within a network of causation would be challenging if done ‘step-by-step’. An analytic tool of great potential to clinical microbiome research is structural equation modelling (SEM), which has a long history of applications to research questions arising within subject areas as diverse as psychology and econometrics. SEM enables postulated models based on a network of causation to be tested en bloc by confrontation with data derived from the literature. Case studies for the potential application of SEM techniques are colonization resistance (CR) and its counterpart, colonization susceptibility (CS), wherein specific microbes within the microbiome are postulated to either impede (CR) or facilitate (CS) invasive infection with pathogenic bacteria. These postulated networks have three causation steps: exposure to specific antimicrobials are key drivers, clinically relevant infection endpoints are the measurable observables and the activity of key microbiome constituents mediating CR or CS, which may be unobservable, appear as latent variables in the model. SEM methods have potential application towards evaluating the activity of specific antimicrobial agents within postulated networks of causation using clinically derived data.