bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Bioperl Toolkit: Perl Modules for the Life Sciences
Authors: Stajich Jason E. , Block David , Boulez Kris , Brenner Steven E. , Chervitz Stephen A. , Dagdigian Chris , Fuellen Georg , Gilbert James G.R. , Korf Ian , Lapp Hilmar , Lehväslaiho Heikki , Matsalla Chad , Mungall Chris J. , Osborne Brian I. , Pocock Matthew R. , Schattner Peter , Senger Martin , Stein Lincoln D. , Stupka Elia , Wilkinson Mark D. , Birney Ewan 
Published: October 2002

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.[Supplemental material is available online at www.genome.org. Bioperl is available as open-source software free of charge and is licensed under the Perl Artistic License (http://www.perl.com/pub/a/language/misc/Artistic.html). It is available for download at http://www.bioperl.org. Support inquiries should be addressed to bioperl-l@bioperl.org.]
Epochs
Authors: Solworth Jon A. 
Published: October 2002

To date, the implementation of message passing languages has required hte communications variables (sometimes called ports) either to be limited to the number of physical communications registers in the machine or to be mapped to memory. Neither solution is satisfactory. Limiting the number of variables decreases modularity and efficiency of parallel programs. Mapping variables to memory increases the cost of communications and the granularity of parallelism. We present here a new programming language construct called
epochs
.

Epochs are a scoping mechanism within which the programmer can declare communications variables, which are live only during the scope of that epoch. To limit the range of time a register has to be allocated for a communications variable, the compiler ensures that all processors enter an epoch simultaneously. The programming style engendered fits somewhere between the SIMD data parallel and the MIMD process spawning models.
We describe an implementation for epochs including an efficient synchronization mechanism, a means of statically binding registers to communications variables, and a method of fusing epochs to reduce synchronization overhead.
Parallel programming with control abstraction
Authors: Crowl Lawrence A. , LeBlanc Thomas J. 
Published: October 2002

Parallel programming involves finding the potential parallelism in an application and mapping it to the architecture at hand. Since a typical application has more potential parallelism than any single architecture can exploit effectively, programmers usually limit their focus to the parallelism that the available control constructs express easily and that the given architecture exploits efficiently. This approach produces programs that exhibit much less parallelism that exists in the application, and whose performance depends critically on the underlying hardware and software.We argue for an alternative approach based oncontrol abstraction. Control abstraction is the process by which programmers define new control constructs, specifying constraints on statement ordering separately from an implementation of that ordering. With control abstraction programmers can define and use a rich variety of control constructs to represent an algorithm's potential parallelism.Since control abstraction separates the definition of a construct from its implementation, a construct may have several different implementations, each exploiting a different subset of the parallelism admitted by the construct. By selecting an implementation for each control construct using annotations, a programmer can vary the parallelism in a program to best exploit the underlying hardware without otherwise changing the source code. This approach produces programs that exhibit most of the potential parallelism in an algorithm, and whose performance can be tuned simply by choosing among the various implementations for the control constructs in use.
Controlled grammatic ambiguity
Authors: Thorup Mikkel 
Published: October 2002

A new approach to ambiguity of context-free grammars is presented, and within this approach the LL and LR techniques are generalized to solve the following problems for large classes of ambiguous grammars:The user may control the parser generation so as to get a parser which finds some specific parse trees for the sentences. The generalized LL and LR techniques will still guarantee that the resulting parser accepts all sentences and terminates in linear time on all input.
Generalizing specifications for uniformly implemented loops
Authors: Dunlop Douglas D. , Basili Victor R. 
Published: October 2002

The problem of generalizing functional specifications for while loops is considered. This problem occurs frequently when trying to verify that an initialized loop satisfies some functional specification, i.e., produces outputs which are some function of the program inputs.
The notion of a valid generalization of a loop specification is defined. A particularly simple valid generalization, a base generalization, is discussed. A property of many commonly occurring while loops, that of being uniformly implemented, is defined. A technique is presented which exploits this property in order to systematically achieve a valid generalization of the loop specification. Two classes of uniformly implemented loops that are particularly susceptible to this form of analysis are defined and discussed. The use of the proposed technique is illustrated with a number of applications. Finally, an implication of the concept of uniform loop implementation for the validation of the obtained generalization is explained.
Systems semantics: principles, applications, and implementation
Authors: Boute Ray 
Published: October 2002

Systems semantics extends the denotational semantics of programming languages to a semantics for the description of arbitrary systems, including objects that are not computations in any sense. By defining different meaning functions, the same formal description may be used to denote different system properties, such as structure, behavior, component cost, and performance aspects (e.g., timing).
The definition of these semantic functions also provides guidance in language design, in particular for the match between language constructs and the system concepts to be expressed. Aiming at compositionality ensures useful properties for formal manipulation. In this fashion, the meaning functions can be made sufficiently simple to serve not only as a direct implementation on a machine but also as rules for reasoning about systems in a transformational manner. As the applications show, however, compositionality can be ensured only through careful consideration of the characteristics of the flow of information inside the system.

Two classes of application are discussed:

Unidirectional systems, in particular digital systems without feedback (combinational) and with feedback (sequential), and a certain class of analog systems.

Nonunidirectional systems, in particular two-port analog networks. The emphasis will be on the functional style of description and on formal reasoning (theorem proving, derivation of properties).

Implementation and rapid prototyping strategies in various system description environments are also briefly discussed. These would permit the concepts of system semantics to be explored without the need for a complete implementation.
Side effects and aliasing can have simple axiomatic descriptions
Authors: Boehm Hans-Juergen 
Published: October 2002

We present a different style of axiomatic definition for programming languages. It is oriented toward imperative languages, such as Algol 68, that do not distinguish between statements and expressions. Rather than basing the logic on a notion of pre- or postcondition, we use the value of a programming language expression as the underlying primitive.
A number of language constructs are examined in this framework. We argue that this style of definition gives us a significantly different view of the notion of “easy axiomatixability.” Side effects in expressions as well as aliasing between variables are shown to be “easily axiomatizable” in our system.
Type extension through polymorphism
Authors: Burton F. Warren 
Published: October 2002

A record data type can be
extended
by addition of more fields. The extended type is a subtype of the original, in that any value of the extended type can be regarded as a value of the original type by ignoring the additional fields. This results in a type hierarchy.

Milner [3] has proposed a polymorphic type system. With the Milner approach, the type of a function may contain type variables. This also results in a type hierarchy.

In a language with a polymorphic type system, if it is anticipated that a record type will need to be extended, then the record type can be defined to have a dummy
extension field
. In the parent type, the extension field will have
null
contents of type
void
. The type of the extension field can differ with different subtypes.

The approach can be extended to allow a type to be subtype of two or more parent types.
To a limited extent, this approach can be used in Ada and other languages with generic program units.
To explore the pathogenesis and scientific connotation of non‐alcoholic fatty liver based on the theory of turbid toxin of traditional Chinese medicine
Authors: Kou Guanjun , Luo Hongwei , Huang Xing , Bai Mingxue , Cao Ke , Ma Hongyu , Lv Xiang 
Published: January 2024

AbstractNon‐alcoholic fatty liver disease (NAFLD) is a metabolic liver disease characterized by the accumulation of excessive liver lipids without alcohol‐induced damage. It has emerged as a significant global health issue. A recent research has indicated that dysregulation of lipid decomposition, uptake, production, oxidation, and secretion causes alterations in various types of lipids, leading to organelle dysfunction and metabolic signaling pathway impairment. Scholars propose that turbid toxin is crucial in the pathogenesis of NAFLD. This article elucidates the meaning of turbid toxin in conjunction with the current literature and analyzes the modern pathophysiological mechanism underlying the development of NAFLD, including turbid toxic substance production, related organelle involvement, biological processes, and pathways, ultimately leading to disease outcomes. The relationship between traditional Chinese medicine and the turbid toxin is also explored to establish a foundation for further mechanistic research on NAFLD.
Unclosing Premature Mortality Gap Among Patients With Gout in the US General Population, Independent of Serum Urate and Atherosclerotic Cardiovascular Risk Factors
Authors: McCormick Natalie , Lin Kehuan , Yokose Chio , Lu Na , Zhang Yuqing , Choi Hyon K. 
Published: January 2024

ObjectiveGout flares are followed by transient major cardiovascular (CV) risk, implicating the role of inflammation; the aim of this study was to determine whether premature mortality rates in patients with gout and CV risk are independent of serum urate (SU) and atherosclerotic CV disease (ASCVD) risk factors.MethodsUsing serial US nationwide prospective cohorts, we evaluated the independent association of prevalent gout with all‐cause and CV mortality, adjusting for SU, ASCVD risk factors, comorbidities, medications, and kidney function and compared mortality rates between the early (1988–1994 baseline) and late cohorts (2007–2016 baseline). We replicated late cohort findings among patients with gout in a nationwide UK cohort (2006–2010 baseline).ResultsAdjusted hazard ratios (HRs) for mortality rates in patients with prevalent gout were similar in early and late US cohorts (1.20 [1.03–1.40] and 1.19 [1.04–1.37], respectively); HRs with further adjustment for SU were 1.19 (1.02–1.38) and 1.19 (1.03–1.37), respectively. Adjusted HR among patients with gout from the UK late cohort was 1.61 (1.47–1.75); these associations were larger among women (P = 0.04) and prominent among Black individuals. Adjusted HR for CV mortality rates in the late US cohort was 1.39 (1.09–1.78); those for circulatory, CV, and coronary heart disease deaths among UK patients with incident gout were 1.48 (1.24–1.76), 1.49 (1.20–1.85), and 1.59 (1.26–1.99), respectively.ConclusionsPatients with gout experience a persistent mortality gap in all‐cause and CV deaths, even adjusting for SU and ASCVD risk factors, supporting a role for gout‐specific pathways (eg, flare inflammation). These findings suggest gaps in current care, particularly in women and possibly among Black patients.image
“What Came First?” Population‐Based Evaluation of Health Care Encounters for Depression and Anxiety Before and After Inflammatory Arthritis Diagnosis: Disentangling the Relationship Between Mental Health and Arthritis
Authors: Howren Alyssa , Sayre Eric C. , Avina‐Zubieta J. Antonio , Puyat Joseph H. , Da Costa Deborah , Xie Hui , Davidson Eileen , De Vera Mary A. 
Published: January 2024

ObjectiveThe study objective was to describe patterns of depression and anxiety health care use before and after diagnosis among patients with inflammatory arthritis (IA), namely, ankylosing spondylitis, psoriatic arthritis, and rheumatoid arthritis.MethodsWe used population‐based linked administrative health data from British Columbia, Canada, to build a cohort of individuals (≥18 years) with incident IA and individuals without IA (“IA‐free controls”) matched on age and sex. We computed the proportion of individuals with IA and controls who had one or more depression or one or more anxiety health care encounters and the use of one or more antidepressants or one or more anxiolytics in each yearly interval five years before and after IA diagnosis. We used multivariable logistic regression models to evaluate the association between IA status and aforementioned depression and anxiety health care use outcomes in each yearly interval.ResultsA total of 80,238 individuals with IA (62.9% female; mean ± SD age 56.2 ± 16.7 years) and 80,238 IA‐free controls (62.9% female; mean ± SD age 56.2 ± 16.6 years) were identified between January 1, 2001, and March 31, 2018. Individuals with IA had significantly increased odds of depression and anxiety health care encounters and dispensation of antidepressants and anxiolytics for each yearly interval before and after diagnosis. Adjusted odds ratios (ORs) were highest in the year immediately before (one or more depression visits: adjusted OR 1.61, 95% confidence interval [CI] 1.55–1.66; one or more anxiolytics: adjusted OR 1.71, 95% CI 1.66–1.77) or after (one or more antidepressants: adjusted OR 1.95, 95% CI 1.89–2.00) IA diagnosis.ConclusionFindings suggest a role for depression and anxiety in characterizing the IA prodrome period and generate hypotheses regarding overlapping biopsychosocial processes that link IA and mental health comorbidities.image
Polyoxometalate‐Structured Materials: Molecular Fundamentals and Electrocatalytic Roles in Energy Conversion
Authors: Ma Tian , Yan Rui , Wu Xizheng , Wang Mao , Yin Bo , Li Shuang , Cheng Chong , Thomas Arne 
Published: January 2024

AbstractPolyoxometalates (POMs), a kind of molecular metal oxide cluster with unique physical–chemical properties, have made essential contributions to creating efficient and robust electrocatalysts in renewable energy systems. Due to the fundamental advantages of POMs, such as the diversity of molecular structures and large numbers of redox active sites, numerous efforts have been devoted to extending their application areas. Up to now, various strategies of assembling POM molecules into superstructures, supporting POMs on heterogeneous substrates, and POMs‐derived metal compounds have been developed for synthesizing electrocatalysts. From a multidisciplinary perspective, the latest advances in creating POM‐structured materials with a unique focus on their molecular fundamentals, electrocatalytic roles, and the recent breakthroughs of POMs and POM‐derived electrocatalysts, are systematically summarized. Notably, this paper focuses on exposing the current states, essences, and mechanisms of how POM‐structured materials influence their electrocatalytic activities and discloses the critical requirements for future developments. The future challenges, objectives, comparisons, and perspectives for creating POM‐structured materials are also systematically discussed. It is anticipated that this review will offer a substantial impact on stimulating interdisciplinary efforts for the prosperities and widespread utilizations of POM‐structured materials in electrocatalysis.
Vicious Cycle‐Breaking Lipid Nanoparticles Remodeling Multicellular Crosstalk to Reverse Liver Fibrosis
Authors: Zhang Ling‐Feng , Deng Wen‐Qi , Huang Qing‐Wen , Zhang Jiao‐Jiao , Wang Yi , Zhou Tian‐Jiao , Xing Lei , Jiang Hu‐Lin 
Published: January 2024

AbstractDuring liver fibrogenesis, the reciprocal crosstalk among capillarized liver sinusoidal endothelial cells (LSECs), activated hepatic stellate cells (HSCs), and dysfunctional hepatocytes constructs a self‐amplifying vicious cycle, greatly exacerbating the disease condition and weakening therapeutic effect. Limited by the malignant cellular interactions, the previous single‐cell centric treatment approaches show unsatisfactory efficacy and fail to meet clinical demand. Herein, a vicious cycle‐breaking strategy is proposed to target and repair pathological cells separately to terminate the malignant progression of liver fibrosis. Chondroitin sulfate‐modified and vismodegib‐loaded nanoparticles (CS‐NPs/VDG) are designed to efficiently normalize the fenestrae phenotype of LSECs and restore HSCs to quiescent state by inhibiting Hedgehog signaling pathway. In addition, glycyrrhetinic acid‐modified and silybin‐loaded nanoparticles (GA‐NPs/SIB) are prepared to restore hepatocytes function by relieving oxidative stress. The results show successful interruption of vicious cycle as well as distinct fibrosis resolution in two animal models through multiregulation of the pathological cells. This work not only highlights the significance of modulating cellular crosstalk but also provides a promising avenue for developing antifibrotic regimens.
Modifying Surface Termination by Bidentate Chelating Strategy Enables 13.77% Efficient Kesterite Solar Cells
Authors: Cao Lei , Wang Lijing , Zhou Zhengji , Zhou Tianxiang , Li Rui , Zhang Hao , Wang Zhiteng , Wu Sixin , Najar Adel , Tian Qingwen , (Frank) Liu Shengzhong 
Published: January 2024

AbstractSurfaces display discontinuities in the kesterite‐based polycrystalline films can produce large defect densities, including strained and dangling bonds. These physical defects tend to introduce electronic defects and surface states, which can greatly promote nonradiative recombination of electron–hole pairs and damage device performance. Here, an effective chelation strategy is reported to suppress these harmful physical defects related to unterminated Cu, Zn, and Sn sites by modifying the surface of Cu2ZnSn(S,Se)4 (CZTSSe) films with sodium diethyldithiocarbamate (NaDDTC). The conjoint theoretical calculations and experimental results reveal that the NaDDTC molecules can be coordinate to surface metal sites of CZTSSe films via robust bidentate chelating interactions, effectively reducing surface undercoordinated defects and passivating the electron trap states. Consequently, the solar cell efficiency of the NaDDTC‐treated device is increased to as high as 13.77% under 100 mW cm−2 illumination, with significant improvement in fill factor and open‐circuit voltage. This surface chelation strategy provides strong surface termination and defect passivation for further development and application of kesterite‐based photovoltaics.
Native Capillary Electrophoresis–Mass Spectrometry of Near 1 MDa Non‐Covalent GroEL/GroES/Substrate Protein Complexes
Authors: Marie Anne‐Lise , Georgescauld Florian , Johnson Kendall R. , Ray Somak , Engen John R. , Ivanov Alexander R. 
Published: January 2024

AbstractProtein complexes are essential for proteins' folding and biological function. Currently, native analysis of large multimeric protein complexes remains challenging. Structural biology techniques are time‐consuming and often cannot monitor the proteins' dynamics in solution. Here, a capillary electrophoresis‐mass spectrometry (CE–MS) method is reported to characterize, under near‐physiological conditions, the conformational rearrangements of ∽1 MDa GroEL upon complexation with binding partners involved in a protein folding cycle. The developed CE–MS method is fast (30 min per run), highly sensitive (low‐amol level), and requires ∽10 000‐fold fewer samples compared to biochemical/biophysical techniques. The method successfully separates GroEL14 (∽800 kDa), GroEL7 (∽400 kDa), GroES7 (∽73 kDa), and NanA4 (∽130 kDa) oligomers. The non‐covalent binding of natural substrate proteins with GroEL14 can be detected and quantified. The technique allows monitoring of GroEL14 conformational changes upon complexation with (ATPγS)4–14 and GroES7 (∽876 kDa). Native CE‐pseudo‐MS3 analyses of wild‐type (WT) GroEL and two GroEL mutants result in up to 60% sequence coverage and highlight subtle structural differences between WT and mutated GroEL. The presented results demonstrate the superior CE–MS performance for multimeric complexes' characterization versus direct infusion ESI–MS. This study shows the CE–MS potential to provide information on binding stoichiometry and kinetics for various protein complexes.