bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Bioinformatics Open Source Conference (BOSC) 2013
Authors: Harris Nomi L , Cock Peter J A , Chapman Brad A , Goecks Jeremy , Hotz Hans-Rudolf , Lapp Hilmar 
Published: January 2018

The 14th annual Bioinformatics Open Source Conference (BOSC) was held in Berlin in July 2013, bringing together over 100 bioinformatics researchers, developers and users of open source software. Since its inception in 2000, BOSC has been organised as a Special Interest Group (SIG) satellite meeting preceding the large International Conference on Intelligent Systems for Molecular Biology (ISMB), which is the annual meeting of the International Society for Computational Biology (ISCB). BOSC provides bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community, and a focused environment for developers and users to interact and share ideas about standards, software development practices, and practical techniques for solving bioinformatics problems. As in previous years, BOSC 2013 was preceded by a Codefest, a two day hackathon that brings together bioinformatics open source project developers and members of the community and allows them to work collaboratively and achieve greater interoperability between tools developed by different groups.
The session topics at BOSC 2013 included several that have been popular in previous years, including Cloud and Parallel Computing, Visualization, Software Interoperability, Genome-scale Data Management, and a session for updates on ongoing open source projects, as well as two new sessions: Translational Bioinformatics, recognizing the growing use of computational biology in medical applications, and Open Science and Reproducible Research. Open Science, a movement dedicated to making all aspects of scientific knowledge production freely available for reuse and extension, not only validates published results by allowing others to reproduce them, but also accelerates the pace of scientific discovery by enabling researchers to more efficiently build on previous work, rather than having to reinvent tools and reassemble data sets.
BOSC typically features two keynote talks by researchers who are influential in some aspect of open source bioinformatics. Our first keynote talk this year was by Cameron Neylon, the Advocacy Director for the Public Library of Science (PLOS), who is a prominent advocate for open science. He discussed the cultural issues that are hindering open science, and how openness in scientific collaborations can generate impact. Our second keynote speaker, Sean Eddy, who is perhaps best known as the author of the HMMER software suite, began his keynote talk with an inspiring history of how he got involved in bioinformatics and proceeded to argue that dedicating effort to thorough engineering in tool development, which is often shunned as incremental, can become the key to creating a lasting impact.
With the increasing reliance of more and more fields of biology on computational tools to manage and analyze their data, BOSC is well positioned to stay relevant to life science, and thus life scientists, for many years to come.
Whale shark (Rhincodon typus) behavior: A multi-year analysis of individuals at Georgia Aquarium
Authors: Black Michael P , Grober Matthew , Schreiber Christian , Coco Chris , Dove Alistair 
Published: January 2018

Background. From the coastal seas near Taiwan to the 6.3 million gallon Ocean Voyager habitat at Georgia Aquarium in Atlanta, Georgia, whale sharks, Rhincodon typus, were brought in stages: two females arrived in June 2006 and two males in June 2007. The behavioral observations described in this study began in 2008 as the first reported observations in captivity to assist in husbandry and better understand whale shark behavior variation between individuals and across time.
Methods. Two types of observations were made of the four sharks currently in the Georgia Aquarium Ocean Voyager habitat: 1) 15-minute focal observations throughout the day of individual sharks from a high gantry vantage point using Stopwatch+ software to time stamp all recorded behavior and 2) observations of swim speed, depth, and swimming direction for all sharks passing by a section of wall over longer periods of time (15 min-hours). Z-tests were used for inter-observer reliability.
Results. For most traits, whale sharks demonstrated unique behavioral profiles that were consistent over many years, but, over the course of years, some of these behavioral traits changed for individual sharks. There were also daily changes in behavior that were consistent across days. For instance, whale sharks showed a clear anticipation of feeding time marked by increases in swimming speed prior to obvious cues of the feed (i.e. 1 hour prior). During observations recorded during the day, whale sharks spent the majority of their time swimming at or near the surface. Most spent relatively equal times swimming clockwise as they did counterclockwise. Swim speeds observed in the habitat were similar to the range of those estimated from work in the field.
Conclusion. Each shark in the habitat demonstrated a behavioral profile unique to that individual, and we have observed short-term and long-term consistent patterns as well as changes in some behavior. These observations increase our knowledge of whale shark behavior, assisting in the husbandry of these animals and giving a better understanding of individual differences, temporal changes, and interactions between sharks.
Three dimensional reconstructions of Nummulites tests reveal complex chamber shapes
Authors: Renema Willem , Cotton Laura 
Published: January 2018

Larger benthic foraminifera (LBF) are an important tool for the biostratigraphy of (sub)tropical shallow marine deposits. In Paleogene the genus Nummulites is an important genus for biostratigraphical zonation schemes. However, classification is Europe centered and based on external characters and equatorial thin sections. New results from regions outside the northern Tethys shows that a more rigid framework for the classification of nummulites is needed.
Here we present a new tool for achieving this goal. We visualise 3D chamber shape of Nummulites djodjokartae and compare these to traditional morphometrical characters. To achieve this goal we use computed microtomography of well preserved Nummulites tests.
We find that despite the regular shape in equatorial and axial thin section 3D chamber shape is not predicted by these sections. We argue that 3D reconstructions of Nummulites tests will be a great aid in improving our understanding lineages within the genus Nummulites, and to elucidate its evolutionary and biogeographical history.
Isolation, identification, and pathological effects of beach sand bacterial extract on human skin keratinocytesin vitro
Authors: Subhan Fazli , Shahzad Raheem , Tauseef Isfahan , Haleem Kashif Syed , Rehman Atta-Ur , Mahmood Sajid , Lee In-Jung 
Published: January 2018

BackgroundBeaches are recreational spots for people. However, beach sand contains harmful microbes that affect human health, and there are no established methods for either sampling and identifying beach-borne pathogens or managing the quality of beach sand.MethodThis study was conducted with the aim of improving human safety at beaches and augmenting the quality of the beach experience. Beach sand was used as a resource to isolate bacteria due to its distinctive features and the biodiversity of the beach sand biota. A selected bacterial isolate termed FSRS was identified asPseudomonas stutzeriusing 16S rRNA sequencing and phylogenetic analysis, and the sequence was deposited in the NCBI GenBank database under the accession numberMF599548. The isolatedP. stutzeribacterium was cultured in Luria–Bertani growth medium, and a crude extract was prepared using ethyl acetate to examine the potential pathogenic effect ofP. stutzerion human skin. A human skin keratinocyte cell line (HaCaT) was used to assess cell adhesion, cell viability, and cell proliferation using a morphological analysis and a WST-1 assay.ResultThe crudeP. stutzeriextract inhibited cell adhesion and decreased cell viability in HaCaT cells. We concluded that the crude extract ofP. stutzeriFSRS had a strong pathological effect on human skin cells.DiscussionBeach visitors frequently get skin infections, but the exact cause of the infections is yet to be determined. The beach sand bacteriumP. stutzerimay, therefore, be responsible for some of the dermatological problems experienced by people visiting the beach.
RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration
Authors: Zhang Jing , Storey Kenneth B. 
Published: January 2018

BackgroundWith the continuous discovery of microRNA’s (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA’s role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis. Therefore, an all-in-one software solution is in demand for a comprehensive yet highly efficient workflow. Here we present RBiomirGS, an R package for a miRNA gene set (GS) analysis.MethodsThe package utilizes multiple databases for target mRNA mapping, estimates miRNA effect on the target mRNAs through miRNA expression profile and conducts a logistic regression-based GS enrichment. Additionally, human ortholog Entrez ID conversion functionality is included for target mRNAs.ResultsBy incorporating all the core steps into one package, RBiomirGS eliminates the need for switching between different software packages. The modular structure of RBiomirGS enables various access points to the analysis, with which users can choose the most relevant functionalities for their workflow.ConclusionsWith RBiomirGS, users are able to assess the functional significance of the miRNA expression profile under the corresponding experimental condition by minimal input and intervention. Accordingly, RBiomirGS encompasses an all-in-one solution for miRNA GS analysis. RBiomirGS is available on GitHub (http://github.com/jzhangc/RBiomirGS). More information including instruction and examples can be found on website (http://kenstoreylab.com/?page_id=2865).
Safety of Simultaneous Vaccination With Adjuvanted Zoster Vaccine and Adjuvanted Influenza Vaccine
Authors: Schmader Kenneth E. , Walter Emmanuel B. , Talaat Kawsar R. , Rountree Wes , Poniewierski Marek , Randolph Emily , Leng Sean X. , Wunderlich Bettina , McNeil Michael M. , Museru Oidda , Broder Karen R. 
Published: October 2024

ImportanceQuadrivalent adjuvanted inactivated influenza vaccine (aIIV4) and adjuvanted recombinant zoster vaccine (RZV) contain novel adjuvants. Data are limited on the comparative safety, reactogenicity, and health-related quality of life (HRQOL) effects of the simultaneous administration of these vaccines.ObjectiveTo compare the safety and reactogenicity after simultaneous doses of RZV and aIIV4 administration (opposite arms) with simultaneous doses of RZV with quadrivalent high-dose inactivated influenza vaccine [HD-IIV4]).Design, Setting, and ParticipantsThis randomized blinded clinical trial was conducted during the 2021-2022 and 2022-2023 influenza seasons at 2 centers in the US among community-dwelling adults aged 65 years or older. Analysis was performed on an intention-to-treat basis.InterventionSimultaneous intramuscular administration of RZV dose 1 and aIIV4 or HD-IIV4 in opposite arms after age stratification (65-69 and ≥70 years) and randomization.Main Outcomes and MeasuresThe primary outcome was the proportions of participants with 1 or more severe solicited reactions during days 1 to 8, using a noninferiority test (10% noninferiority margin). Additional measures included serious adverse events and adverse events of clinical interest during days 1 to 43 of the study period.ResultsA total of 267 adults (median age, 71 years [range, 65-92 years]; 137 men [51.3%]) were randomized; 130 received simultaneous RZV and aIIV4, and 137 received simultaneous RZV and HD-IIV4. The proportion of patients reporting 1 or more severe reactions after simultaneous administration of RZV and aIIV4 (15 of 115 [11.5%]) was noninferior compared with simultaneous RZV and HD-IIV4 (17 of 119 [12.5%]) (absolute difference, −1.0% [95% CI, −8.9% to 7.1%]). There were no significant differences in the number of serious adverse events or adverse events of clinical interest between the groups.Conclusions and RelevanceIn this clinical trial of simultaneous doses of RZV and aIIV4 compared with simultaneous doses of RZV and HD-IIV4, overall safety findings were similar between groups. From a safety standpoint, this study supports the simultaneous administration of RZV and aIIV4 among older adults.Trial RegistrationClinicalTrials.gov Identifier: NCT05007041
Prolonging Endothelial Cell Survival with Thermoresponsive Peptide‐Functionalized Hydrogels Improves Ischemic Limb Tissue Regeneration and Function
Authors: Wang Huifeng , Dang Caitlyn , Rivera‐Bolanos Nancy , Tong Ophelia , Wang Xinlong , Chen Guo , Riter Rebecca L. , Chin Yuan‐Ho , Duan Chongwen , Zhang Xiaomin , Haney Chad R. , Ameer Guillermo , Jiang Bin 
Published: October 2024

AbstractCritical limb ischemia (CLI) presents a significant clinical challenge, leading to tissue ischemia and potentially resulting in limb necrosis or amputation. Cell‐based regenerative therapies offer promise for improving outcomes in CLI, but their effectiveness is often limited by poor cell survival and engraftment. This study hypothesized that a thermo‐responsive polymer, poly(polyethylene glycol citrate‐co‐N‐isopropylacrylamide) (PPCN), combined with pro‐survival bioactive peptides, can create a protective microenvironment to improve endothelial cell survival and function after their delivery. Through in vitro and in vivo experiments, laminin‐derived peptide A5G81 and vascular endothelial growth factor (VEGF)‐derived peptide QK are identified as effective in promoting endothelial cell spreading, proliferation, and prolonged survival. PPCN's viscoelastic properties protected against shear stress during injection, while the peptides supported endothelial cell behavior through distinct molecular pathways. Importantly, delivery of endothelial cells with PPCN‐A5G81 and PPCN‐QK in a murine hindlimb ischemia model resulted in significant improvements in limb perfusion, tissue preservation, and functional outcomes compared to controls. Additionally, this approach enhanced skeletal muscle remodeling following ischemic injury. This innovative biomaterial platform represents a versatile solution for addressing cell survival challenges and advancing regenerative therapies in CLI and other ischemic conditions.
Stabilizing 2D Pt‐Based Halide Perovskites via Solvent Lone Pair Donation
Authors: Liu Huilong , Biswas Maitreyo , Smith Walter J. , Barnard Edward , Beechem Thomas , Mannodi‐Kanakkithodi Arun , Bansal Shubhra 
Published: October 2024

AbstractPlatinum‐based halide perovskites exhibit promising optoelectronic properties along with merits of low‐temperature processing and stability. Current research on Pt halide perovskites is limited to 0D A2BX6 structure as the ABX3 3D structure is thermodynamically unstable. Herein, the study reports the stabilization of the ABX3 structure into a 2D layered phase, CsPtI3(DMSO), that is stable up to 181.5 °C. The 2D phase shows an excitonic peak at the absorption edge of 600 nm, indicating quantum confinement. It also exhibits a large Stokes shift due to intersystem crossing (ISC), with a quenched singlet excitonic fluorescence at 610 nm and strong triplet emission at 852 nm. Pt(II) co‐ordinates with dimethyl sulfoxide (DMSO) via σ‐donation of S lone‐pair electrons and π‐ back donation from Pt to S, stabilizing CsPtI3(DMSO) layered structure. The strong electronic interaction between DMSO and Pt(II) and orbital mixing lead to spin‐orbit‐coupling, facilitating ISC and singlet‐to‐triplet exciton energy transfer. The interaction of Pt and DMSO is further confirmed by addition of thioacetamide (TAA), a strong S‐donor, which retards the formation of 2D layered structure, and directly results in Cs2PtI6 and Pt.
Electronic Modulation of RuCo Catalysts on TiO2 Nanotubes Promoting Durable Acidic Overall Water Splitting
Authors: Chen Hengyi , Gao Zehua , Ren Shijie , Gao Rui‐Ting , Wu Limin , Wang Lei 
Published: October 2024

AbstractThe development of efficient and durable bifunctional electrocatalysts is essential for hydrogen production from acidic water splitting. Herein, a TiO2 nanotube‐loaded Co‐doped Ru nanoparticle catalyst (RuCo/TiO2 NTs) is reported that exhibits excellent activity and stability toward acidic oxygen evolution reaction (OER) and hydrogen evolution reaction (HER). The Ru─O─Ti bonding is enhanced by Co doping, and the metal carrier interaction between Ru nanoparticles and TiO2 NTs is enhanced, which effectively stabilizes Ru species during OER and initiates hydrogen spillover accelerating HER kinetics. As a result, RuCo/TiO2 NTs catalyst requires only 156 mV OER overpotential and 17 mV HER overpotential to achieve a current density of 10 mA cm−2 with a stability more than 500 h in acidic conditions. More importantly, benefiting from the excellent bifunctional activities, the proton exchange membrane electrolyte assembled from RuCo/TiO2 NTs has excellent activity and robust stability (1000 h). This work opens a new avenue for the efficient energy conversion devices.
Co‐inoculation with Rhizobium, Azospirillum, and microalgae increases common bean yield and profitability
Authors: de Oliveira Karen Sinéia , Volsi Bruno , Telles Tiago Santos , Mendes Aretusa Daniela Resende , Yunes João Sarkis , Andrade Diva Souza 
Published: October 2024

AbstractWidely used as inoculants in agriculture, nitrogen‐fixing bacteria can be associated with other plant growth‐promoting microorganisms (PGPMs) to increase crop grain yield. This study aimed to evaluate whether co‐inoculation with Rhizobium tropici and Azospirillum brasilense associated with microalgae or cyanobacteria enhances common bean (Phaseolus vulgaris) grain yield and its economic gains in contrasting sandy and clayey soils. Water‐soluble protein content and indole‐3‐acetic acid (IAA) production of two cyanobacteria (Anabaena cylindrica and Calotrix brevissima) and six Chlorophyta microalgae (Nannochloropsis oculata, Haematococcus pluvialis, Muriellopsis sphaerica, Chlorella protothecoides, Chlorella vulgaris, and Botryococcus braunii) were determined. Anabaena cylindrica and C. brevissima had the highest IAA production, 336.7 ± 44.7 and 94.1 ± 11.8 µg IAA mg−1 of protein, respectively. Two field experiments were carried out to evaluate the triple inoculation of these Chlorophyta microalgae and cyanobacteria associated with R. tropici plus A. brasilense on the agronomic efficiency and profitability of common bean. Co‐inoculation of C. vulgaris plus R. tropici and A. brasilense in common bean had grain yield of 1277.5 kg ha−1 in clayey soil and 2960.3 kg ha−1 in sandy soil, increasing by 219.7 and 656.0 kg ha−1, respectively, in relation to double inoculation of R. tropici + A. brasilense. In the sandy soil, common bean with triple co‐inoculation had the highest profit ($956 ha−1), which was 25.6% higher than the N fertilized plants. Co‐inoculation with PGPMs generated the highest economic gains, and in addition, it is an eco‐friendly agronomic practice for sustainable food production.
Direct Epitaxial Growth of Polycrystalline MOF Membranes on Cu Foils for Uniform Li Deposition in Long‐life Anode‐free Li Metal Batteries
Authors: Wu Haiyang , Wu Langyuan , Li Yang , Dong Wendi , Ma Wenyu , Li Shaopeng , Xiao Dewei , Huang Peng , Zhang Xiaogang 
Published: October 2024

AbstractAnode‐free Li‐metal battery (AFLMB) is being developed as the next generation of advanced energy storage devices. However, the low plating and stripping reversibility of Li on Cu foil prevents its widespread application. A promising avenue for further improvement is to enhance the lithophilicity of Cu foils and optimise their surfaces through a metal–organic framework (MOF) functional layer. However, excessive binder usage in the current approaches obscures the active plane of the MOF, severely limiting its performance. In response to this challenge, MOF polycrystalline membrane technology has been integrated into the field of AFLMB in this work. The dense and seamless HKUST‐1 polycrystalline membrane was deposited on Cu foil (HKUST‐1 M@Cu) via an epitaxial growth strategy. In contrast to traditional MOF functional layers, this binder‐free polycrystalline membrane fully exposes lithophilic sites, effectively reducing the nucleation overpotential and optimising the deposition quality of Li. Consequently, the Li plating layer becomes denser, eliminating the effects of dendrites. When coupled with LiFePO4 cathodes, the battery based on the HKUST‐1 membrane exhibits excellent rate performance and cycling stability, achieving a high reversible capacity of approximately 160 mAh g−1 and maintaining a capacity retention of 80.9 % after 1100 cycles.
Sensitive and Cost‐Effective Tools in the Detection of Ovarian Cancer Biomarkers
Authors: Elhami Anis , Mobed Ahmad , Soleimany Reza , Yazdani Yalda , Kazemi Esmat Sadat , Mohammadi Mahya , Saffarfar Hossein 
Published: October 2024

ABSTRACTWomen diagnosed with late‐stage ovarian cancer suffer a very high rate of mortality. Accordingly, it is imperative to detect and diagnose the disease as early as possible in its development. Achievement of this aim implies relatively large‐scale screening of women at an age of clinical significance through assay of biomarkers for disease present in blood or serum. Biosensor detection offers an attractive technology for the automated detection of such species. Among several biomarkers that have been identified that are present in patients with ovarian cancer, the only one that is commonly tested for in clinical use is cancer antigen 125, which is considered to be a poor biomarker for the disease. Here, we describe several biosensors that developed in the past decade for the detection of ovarian cancer biomarkers such as CA125, human epididymis protein 4 (HE4) and apolipoprotein A1. The challenges presented by the fabrication of biosensor devices for detecting ovarian cancer and the limited number of biosensors developed for this purpose are discussed.