bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selecting signature oligonucleotides to identify
organisms using DNA arrays
Authors: Kaderali Lars , Schliep Alexander 
Published: October 2002

Abstract
Motivation: DNA arrays are a very useful tool to quickly identify biological agents present in some given sample, e.g. to identify viruses causing disease, for quality control in the food industry, or to determine bacteria contaminating drinking water. The selection of specific oligos to attach to the array surface is a relevant problem in the experiment design process. Given a set S of genomic sequences (the target sequences), the task is to find at least one oligonucleotide, called probe, for each sequence in S. This probe will be attached to the array surface, and must be chosen in a way that it will not hybridize to any other sequence but the intended target. Furthermore, all probes on the array must hybridize to their intended targets under the same reaction conditions, most importantly at the temperature T at which the experiment is conducted.
Results: We present an efficient algorithm for the probe design problem. Melting temperatures are calculated for all possible probe–target interactions using an extended nearest-neighbor model, allowing for both non-Watson–Crick base-pairing and unpaired bases within a duplex. To compute temperatures efficiently, a combination of suffix trees and dynamic programming based alignment algorithms is introduced. Additional filtering steps during preprocessing increase the speed of the computation.
The practicability of the algorithms is demonstrated by two case studies: The identification of HIV-1 subtypes, and of 28S rDNA sequences from ≥400 organisms.
Availability: The software is available on request.
Contact: kaderali@zpr.uni-koeln.de
* To whom correspondence should be addressed.
Genquire: genome annotation browser/editor
Authors: Wilkinson M.D. , Block D. , Crosby W.L. 
Published: October 2002

Abstract
Summary: We present a software package, Genquire, that allows visualization, querying, hand editing, and de novo markup of complete or partially annotated genomes. The system is written in Perl/Tk and uses, where possible, existing BioPerl data models and methods for representation and manipulation of the sequence and annotation objects. An adaptor API is provided to allow Genquire to display a wide range of databases and flat files, and a plugins API provides an interface to other sequence analysis software.
Availability: Genquire v3.03 is open-source software. The code is available for download and/or contribution at http://www.bioinformatics.org/Genquire
Contact: mwilkinson@gene.pbi.nrc.ca
* To whom correspondence should be addressed. Present address: Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
Genexp—a genetic network simulation environment
Authors: Vu Tra Thi , Vohradsky Jiri 
Published: October 2002

Abstract
Summary: An environment for simulation of dynamics of genetic regulatory networks is presented. The model is based on the recurrent neural network principle and allows to interactively simulate various genetic regulatory interactions under different features of the system. The results are displayed graphically.
Availability: http://proteom.biomed.cas.cz/genexp
Contact: vohr@biomed.cas.cz
* To whom correspondence should be addressed.
INTERFERENCE AND DECOHERENCE OF COMPOSITE FERMIONS IN THE QUANTUM HALL EFFECT
Authors: STERN A. 
Published: October 2002

In this talk I will discuss quantum interference phenomena of composite fermions in quantum Hall systems. In particular, I will focus on huge mesoscopic fluctuations of non-linear response and of Coulomb drag in single and bi-layer systems. Finally, I will give a simple physical picture of dephasing (de-coherence) of composite fermions, with simple expressions for their coherence length. Most of the talk will be based on work done in collaboration with I. Aleiner and B. Narozhny (Stony Brook).
Concordance in Medical Urgency Classification of Discharge Diagnoses and Reasons for Visit
Authors: Giannouchos Theodoros V. , Ukert Benjamin , Wright Brad 
Published: January 2024

ImportanceCurrent policies to divert emergency department (ED) visits for less medically urgent conditions to more cost-effective settings rely on retrospective adjudication of discharge diagnoses. However, patients present to the ED with concerns, making it challenging for clinicians.ObjectiveTo characterize ED visits based on the medical urgency of the presenting reasons for visit and to explore the concordance between discharge diagnoses and reasons for visit.Design, Setting, and ParticipantsIn this retrospective, cross-sectional study, a nationwide sample of ED visits by adults (aged ≥18 years) in the US from the 2018 and 2019 calendar years’ ED data of the National Hospital Ambulatory Medical Care Survey was used. An algorithm to probabilistically assign ED visits into medical urgency categories based on the presenting reason for visit was developed. A 3-step, look-back method was applied using an updated version of the New York University ED algorithm, and a map of all possible discharge diagnoses to the same reasons for visit was developed. Analyses were conducted in July and August 2023.Main Outcomes and MeasuresThe main outcome was probabilistic medical urgency classification of reasons for visits and discharge diagnoses and their concordance.ResultsWe analyzed 27 068 ED visits (mean age, 48.2% years [95% CI, 47.5%-48.9% years]) representing 190.7 million visits nationwide. Women (mean, 57.0% [95% CI, 55.9%-58.1%]) and patients with public health insurance coverage, including Medicare (mean, 24.9% [95% CI, 21.9%-28.0%]) and Medicaid (mean, 25.1% [95% CI, 21.0%-29.2%]), accounted for the largest share of ED visits, and a mean of 13.2% (95% CI, 11.4%-15.0%) of all visits resulted in a hospital admission. Overall, about 38.5% and 53.9% of all ED visits were classified with 100% and 75% probabilities, respectively, as injury related, emergency care needed, emergent but primary care treatable, nonemergent, or mental health or substance use disorders related based on discharge diagnosis compared with 0.4% and 12.4%, respectively, of all encounters based on patients’ reason for visit. Among discharge diagnoses assigned with high certainty to only 1 urgency category using the New York University ED algorithm, between 38.0% (95% CI, 36.3%-39.6%) and 57.4% (95% CI, 56.0%-58.8%) aligned with the probabilistic categorical assignments of their corresponding reasons for visit.Conclusions and RelevanceIn this cross-sectional study of 190.7 million ED visits among adults aged 18 years or older, a smaller percentage of reasons for visit could be prospectively categorized with high accuracy to a specific medical urgency category compared with all visits based on discharge diagnoses, and a limited concordance between reasons for visit and discharge diagnoses was found. Alternative methods are needed to identify the medical necessity of ED encounters more accurately.
Funding for Refugee Health Research From the National Institutes of Health Between 2000 and 2020
Authors: Kaur Mehak , Bridi Lana , Kaki Dahlia , Albahsahli Behnan , Bencheikh Nissma , Saadi Altaf , Bandoli Gretchen , Anderson Cheryl A.M. , Sideman Alissa Bernstein , Al-Rousan Tala 
Published: January 2024

ImportanceThe US has historically resettled more refugees than any other country, with over 3.5 million refugees since 1980. The National Institutes of Health (NIH) is the largest public funder of biomedical research and development, but its role in mitigating many health disparities refugees experience through its funded research remains unknown.ObjectiveTo examine the NIH’s research funding patterns on refugee health research over the last 2 decades.Design, Setting, and ParticipantsSecondary analysis of NIH-funded grants between 2000 and 2020 using a cross-sectional study design. The NIH Research Portfolio Online Reporting Tools database was used to find relevant grants. Data were analyzed from November 2021 to September 2022.Main Outcomes and MeasuresNIH grants awarded by year, state, grant type, research area, funding institute, grant duration, and amount funded.ResultsOf 1.7 million NIH grants funded over the 20-year study period, only 78 addressed refugee health. Funded grants were mostly training grants (23 grants [29%]), followed by hypothesis-driven research (R01 grants; 22 grants [28%]), pilot or preliminary investigation proposals (13 grants [17%]), and other types of grants (20 grants [26%]). The most studied research domain was mental health (36 grants [46%]), followed by refugee family dynamics and women’s and children’s health (14 grants [18%]). A total of 26 grants (33%) were funded by the National Institute of Mental Health and 15 (19%) were funded by the National Institute of Child Health and Human Development. Most grants were US-based (60 grants [76%]) and the state of Massachusetts received the greatest amount of funding ($14 825 852 [18%]). In 2020, the NIH allocated about $2.3 million to refugee health research, or less than 0.01% of its $42 billion budget that year. The number of grants funded in each time period did not always reflect changes in the number of refugees resettled in the US over the years.Conclusions and RelevanceThis cross-sectional study found that there remain significant gaps in the understanding of and interventions in the health research needs of refugees locally and along the migratory route. To close these gaps, the NIH should increase its investments in comprehensive studies assessing the physical, mental, and social well-being of this expanding population. This can be achieved by ensuring that all NIH institutes allocate budgets specifically for refugee health research and extend support for the training of refugee researchers.
Fat Body Mass and Vertebral Fracture Progression in Women With Breast Cancer
Authors: Cosentini Deborah , Pedersini Rebecca , Di Mauro Pierluigi , Zamparini Manuel , Schivardi Greta , Rinaudo Luca , Di Meo Nunzia , Delbarba Andrea , Cappelli Carlo , Laganà Marta , Alberti Andrea , Baronchelli Maria , Guerci Greta , Laini Lara , Grisanti Salvatore , Simoncini Edda Lucia , Farina Davide , Mazziotti Gherardo , Berruti Alfredo ,   Bone Health Group of the ASST Spedali Civili, Brescia, Boglioni Monica , Calzoni Giulia 
Published: January 2024

ImportanceWomen with early breast cancer (EBC) exposed to aromatase inhibitors (AIs) may experience fragility fractures despite treatment with bone-active drugs. Risk factors for fractures in patients receiving AIs and denosumab have not been explored to date.ObjectivesTo evaluate whether an association exists between dual x-ray absorptiometry (DXA)–measured fat body mass (FBM) and vertebral fracture (VF) progression in postmenopausal women with EBC undergoing adjuvant therapy with AIs in combination with denosumab and to examine whether VF was associated with common risk factors for bone fracture and parameters of body composition other than FBM.Design, Setting, and ParticipantsFor this prospective, single-center, cohort study, 237 patients with EBC who were undergoing adjuvant treatment with AIs and denosumab (60 mg every 6 months) were enrolled at the Breast Unit of the ASST Spedali Civili of Brescia from September 2014 to June 2018. Data analysis was conducted in June 2022.ExposureBody composition parameters, bone mineral density, and morphometric VFs were assessed by DXA at study entry and after 18 months of therapy.Main Outcomes and MeasuresVF progression, defined as either new or worsening of preexisting VFs, between the 2 time points.ResultsOf the 237 patients enrolled (median [range] age, 61 [28-84] years), 17 (4.4%) reported VF progression. Univariable analysis found an association between VF progression and a history of clinical fractures (odds ratio [OR], 3.22; 95% CI, 1.19-8.74; P = .02), Fracture Risk Assessment Tool (FRAX) score for major fractures (OR, 4.42; 95% CI, 1.23-13.79; P = .04), percentage of FBM (OR, 6.04; 95% CI, 1.69-21.63; P = .006), and android fat (OR, 9.58; 95% CI, 1.17-78.21; P = .04) and an inverse association with appendicular lean mass index–FBM ratio (OR, 0.25, 95% CI, 0.08-0.82; P = .02). Multivariable analysis revealed percentage of FBM (OR, 5.41; 95% CI, 1.49-19.59; P = .01) and FRAX score (OR, 3.95; 95% CI, 1.09-14.39; P = .04) as independent variables associated with VF progression.Conclusions and RelevanceThe findings of this study suggest that baseline FBM is an independent factor for VF progression in patients with EBC treated with adjuvant AIs and denosumab. This observation is new and indicates that diet and exercise may synergize with denosumab in the management of bone health in this patient setting.
Population-Based Validation of the MIA and MSKCC Tools for Predicting Sentinel Lymph Node Status
Authors: Olofsson Bagge Roger , Mikiver Rasmus , Marchetti Michael A. , Lo Serigne N. , van Akkooi Alexander C. J. , Coit Daniel G. , Ingvar Christian , Isaksson Karolin , Scolyer Richard A. , Thompson John F. , Varey Alexander H. R. , Wong Sandra L. , Lyth Johan , Bartlett Edmund K. 
Published: January 2024

ImportancePatients with melanoma are selected for sentinel lymph node biopsy (SLNB) based on their risk of a positive SLN. To improve selection, the Memorial Sloan Kettering Cancer Center (MSKCC) and Melanoma Institute Australia (MIA) developed predictive models, but the utility of these models remains to be tested.ObjectiveTo determine the clinical utility of the MIA and MSKCC models.Design, Setting, and ParticipantsThis was a population-based comparative effectiveness research study including 10 089 consecutive patients with cutaneous melanoma undergoing SLNB from the Swedish Melanoma Registry from January 2007 to December 2021. Data were analyzed from May to August 2023.Main Outcomes and Measures,The predicted probability of SLN positivity was calculated using the MSKCC model and a limited MIA model (using mitotic rate as absent/present instead of count/mm2 and excluding the optional variable lymphovascular invasion) for each patient. The operating characteristics of the models were assessed and compared. The clinical utility of each model was assessed using decision curve analysis and compared with a strategy of performing SLNB on all patients.ResultsAmong 10 089 included patients, the median (IQR) age was 64.0 (52.0-73.0) years, and 5340 (52.9%) were male. The median Breslow thickness was 1.8 mm, and 1802 patients (17.9%) had a positive SLN. Both models were well calibrated across the full range of predicted probabilities and had similar external area under the receiver operating characteristic curves (AUC; MSKCC: 70.8%; 95% CI, 69.5-72.1 and limited MIA: 69.7%; 95% CI, 68.4-71.1). At a risk threshold of 5%, decision curve analysis indicated no added net benefit for either model compared to performing SLNB for all patients. At risk thresholds of 10% or higher, both models added net benefit compared to SLNB for all patients. The greatest benefit was observed in patients with T2 melanomas using a threshold of 10%; in that setting, the use of the nomograms led to a net reduction of 8 avoidable SLNBs per 100 patients for the MSKCC nomogram and 7 per 100 patients for the limited MIA nomogram compared to a strategy of SLNB for all.Conclusions and RelevanceThis study confirmed the statistical performance of both the MSKCC and limited MIA models in a large, nationally representative data set. However, decision curve analysis demonstrated that using the models only improved selection for SLNB compared to biopsy in all patients when a risk threshold of at least 7% was used, with the greatest benefit seen for T2 melanomas at a threshold of 10%. Care should be taken when using these nomograms to guide selection for SLNB at the lowest thresholds.
In‐Sensor Passive Speech Classification with Phononic Metamaterials
Authors: Dubček Tena , Moreno‐Garcia Daniel , Haag Thomas , Omidvar Parisa , Thomsen Henrik R. , Becker Theodor S. , Gebraad Lars , Bärlocher Christoph , Andersson Fredrik , Huber Sebastian D. , van Manen Dirk‐Jan , Villanueva Luis Guillermo , Robertsson Johan O.A. , Serra‐Garcia Marc 
Published: January 2024

AbstractMitigating the energy requirements of artificial intelligence requires novel physical substrates for computation. Phononic metamaterials have vanishingly low power dissipation and hence are a prime candidate for green, always‐on computers. However, their use in machine learning applications has not been explored due to the complexity of their design process. Current phononic metamaterials are restricted to simple geometries (e.g., periodic and tapered) and hence do not possess sufficient expressivity to encode machine learning tasks. A non‐periodic phononic metamaterial, directly from data samples, that can distinguish between pairs of spoken words in the presence of a simple readout nonlinearity is designed and fabricated, hence demonstrating that phononic metamaterials are a viable avenue towards zero‐power smart devices.
Ether‐Based Electrolyte for High‐Temperature and High‐Voltage Lithium Metal Batteries
Authors: Xu Tonghui , Zheng Tianle , Ru Zhengzheng , Song Jinhua , Gu Meirong , Yue Ye , Xiao Yiyao , Amzil Said , Gao Jie , Müller‐Buschbaum Peter , Wang Ke , Zhao Hongbin , Cheng Ya‐Jun , Xia Yonggao 
Published: January 2024

AbstractThe compatibility of lithium metal with organic solvents is the most crucial for lithium metal batteries (LMBs). Even though ether solvents show excellent compatibility toward lithium metal, the reactivity of the ether solvents at elevated temperatures and high voltages hinders their utilization in lithium metal battery systems. In this study, a high‐temperature ether electrolyte is designed comprising lithium oxalyldifluoroborate (LiODFB), diethylene glycol dibutyl ether (DGDE), 3‐methoxypropionitrile (MPN), and fluorinated ethylene carbonate (FEC), which is abbreviated as MDF electrolyte. The presence of MPN in the electrolyte changes the solvation structure, thereby facilitating increased redox reactions of ODFB− and synergizing with FEC to build a robust solid electrolyte interface (SEI), effectively inhibiting lithium dendrites growth and solvent decomposition. Consequently, the MDF electrolyte exhibits not only long cyclic stability and high coulombic efficiency in Li||Cu and Li||Li cells but also excellent cyclic characteristics in both Li||LiFePO4 (LFP) and Li||LiNi0.8Co0.1Mn0.1O2 (NCM811) cells. Remarkably, these cells demonstrate stable operation even when exposed to higher temperatures of up to 80 °C, while the Li||NCM811 cell maintains consistent cyclic stability at an elevated voltage level of 4.5 V.
High‐Content Carbon Layer Confined Small‐Molecule/Covalent Sulfur Cathode Enables Long‐Life Calcium–Sulfur Batteries in Hybrid‐Ion Electrolyte
Authors: Wu Shuang , Jiang Zuobei , Wu Canhong , Li Haitao , Huang Junxi , Li Na , Huang Shaoming 
Published: January 2024

AbstractCalcium‐sulfur (Ca‐S) battery is a promising candidate for large‐scale energy storage system. However, the development of long‐life room‐temperature Ca–S batteries is hindered by the lack of effective sulfur cathode and the incompatibility between electrodes and electrolytes, leading to irreversible sulfur conversion, inefficient calcium plating/stripping and improper cathode/anode‐electrolyte interfaces (CEI/SEI). Herein, a turbo carbon layer confined small‐molecule/covalent sulfur cathode (S@C NS) with a record‐high content of 65.7% and enlarged carbon layer space is prepared via a C/S co‐deposition process. By using such a cathode and optimizing interfacial electrochemistry in LiPF6/Ca(BF4)2‐based hybrid electrolyte, a record‐breaking long‐life room‐temperature Ca‐S battery is reported. The capacity reaches 824.6 mAh g−1 at 100 mA g−1 with a retention of 47.9% after 145 cycles, and 462.1 mAh g−1 at even 500 mA g−1. Mechanism studies demonstrated that a Li/Ca‐based hybrid CEI with porous microstructure is found to facilitate the transfer kinetics of Ca2+ across the CEI; Turbo carbon layers with large inter‐layer space and their strong confinement on small‐molecule sulfur enabled reversible solid‐state sulfur conversion in situ inside the cathode; An effective Li/Ca‐based hybrid SEI formed on anode, allowing reversible Ca plating/stripping with low deposition potential and small overpotential.
DTBDT‐Based Polymer Hole Transport Materials for Low Voltage Loss CsPbI2Br Perovskite Solar Cells
Authors: Duan Chen , Tang Ailing , Guo Qiang , Zhang Weilin , Yang Lei , Ding Yuanjia , Dai Zheng , Zhou Erjun 
Published: January 2024

AbstractThe power conversion efficiency (PCE) of CsPbI2Br perovskite solar cells (PSCs) is still far from the theoretical efficiency due to the pronounced losses in open‐circuit voltage (VOC). The VOC loss can be mitigated by employing an appropriate hole transport layer (HTL), which facilitates energy level alignment and minimizes interface recombination losses. In this work, two D‐π‐A type polymers are chosen, PE64 and PE65, as HTLs, where pentacyclic dithieno[2,3‐d; 2′,3′‐d “]benzo[1,2‐b; 4,5‐b”]dithiophene (DTBDT) as the D‐unit and quinoxaline (Qx) as the A‐unit. It is demonstrated that the polymer PE65 with chlorinated thiophene side chain on the DTBDT unit has an optimized molecular arrangement, improved energy level matching, and enhanced passivation with CsPbI2Br, effectively reducing the losses caused by radiative and non‐radiative recombination in CsPbI2Br PSCs. Finally, the CsPbI2Br PSCs utilizing PE65 as HTL achieve a power conversion efficiency (PCE) of 17.60% with a high VOC of 1.44 V. Furthermore, the PE64 and PE65 are also employed to construct inter‐connecting layers (ICLs) for tandem solar cells (TSCs). The CsPbI2Br/D18:Y6 TSCs based on PE65‐ICL yield a PCE of 22.32% with a high VOC of 2.25 V. This work demonstrates that pentacyclic DTBDT‐based polymers are also promising HTLs for high‐performance PSCs and TSCs.
Injectable Mesh‐Like Conductive Hydrogel Patch for Elimination of Atrial Fibrillation
Authors: Dai Jing , Wang Bingfang , Chang Zhiqiang , Lu Xinxin , Nie Jianfang , Ren Qinjuan , Lv Yingying , Rotenberg Menahem Y. , Fang Yin 
Published: January 2024

AbstractIrregular electrical impulses in atrium are the leading cause of atrial fibrillation (AF), resulting in fatal arrhythmia and sudden cardiac death. Traditional medication and physical therapies are widely used, but generally suffer problems in serious physical damage and high surgical risks. Flexible and soft implants have great potential to be a novel approach for heart diseases therapy. A conductive hydrogel‐based mesh cardiac patch is developed for application in AF elimination. The designed mesh patch with rhombic‐shaped structure exhibits excellent flexibility, surface conformability, and deformation compliance, making it fit well with heart surface and accommodate to the deformation during heart beating. Moreover, the mechanical elastic and shape‐memory properties of the mesh patch enable a minimally invasive injection of the patch into living animals. The mesh patch is implanted on the atrium surface for one month, indicating good biocompatibility and stability. Furthermore, the conductive patch can effectively eliminate AF owing to the conductivity and high charge storage capability (CSC) of the hydrogel. The proposed scheme of cardiac bioelectric signal modulation using conductive hydrogel brings new possibility for the treatment of arrhythmia diseases.