bluuebunny/crossref_metadata_2025_split huggingface dataset:
Six-fold speed-up of Smith–Waterman sequence database
searches using parallel processing on common microprocessors
Authors: Rognes Torbjørn , Seeberg Erling 
Published: July 2002

Abstract
Motivation: Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith–Waterman. However, because of the computationally demanding nature of this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has been obtained at the cost of reduced sensitivity or very expensive hardware.
Results: A fast implementation of the Smith–Waterman sequence-alignment algorithm using Single-Instruction, Multiple-Data (SIMD) technology is presented. This implementation is based on the MultiMedia eXtensions (MMX) and Streaming SIMD Extensions (SSE) technology that is embedded in Intel’s latest microprocessors. Similar technology exists also in other modern microprocessors. Six-fold speed-up relative to the fastest previously known Smith–Waterman implementation on the same hardware was achieved by an optimized 8-way parallel processing approach. A speed of more than 150 million cell updates per second was obtained on a single Intel Pentium III 500 MHz microprocessor. This is probably the fastest implementation of this algorithm on a single general-purpose microprocessor described to date.
Availability: Online searches with the software are available at http://dna.uio.no/search/
Contact: torbjorn.rognes@labmed.uio.no
To whom correspondence should be addressed.
Multi-class protein fold recognition using support vector

machines and neural networks
Authors: Ding Chris H.Q. , Dubchak Inna 
Published: July 2002

Abstract
Motivation: Protein fold recognition is an important approach to structure discovery without relying on sequence similarity. We study this approach with new multi-class classification methods and examined many issues important for a practical recognition system.
Results: Most current discriminative methods for protein fold prediction use the one-against-others method, which has the well-known ‘False Positives’ problem. We investigated two new methods: the unique one-against-others and the all-against-all methods. Both improve prediction accuracy by 14–110% on a dataset containing 27 SCOP folds. We used the Support Vector Machine (SVM) and the Neural Network (NN) learning methods as base classifiers. SVMs converges fast and leads to high accuracy. When scores of multiple parameter datasets are combined, majority voting reduces noise and increases recognition accuracy. We examined many issues involved with large number of classes, including dependencies of prediction accuracy on the number of folds and on the number of representatives in a fold. Overall, recognition systems achieve 56% fold prediction accuracy on a protein test dataset, where most of the proteins have below 25% sequence identity with the proteins used in training.
Supplementary information: The protein parameter datasets used in this paper are available online (http://www.nersc.gov/~cding/protein).
Contact: chqding@lbl.gov; ildubchak@lbl.gov
* To whom correspondence should be addressed.
ATV: display and manipulation of annotated phylogenetic trees
Authors: Zmasek Christian M. , Eddy Sean R. 
Published: July 2002

Abstract
Summary: A Tree Viewer (ATV) is a Java tool for the display and manipulation of annotated phylogenetic trees. It can be utilized both as a standalone application and as an applet in a web browser.
Availability: ATV is available via WWW at http://www.genetics.wustl.edu/eddy/atv/ and via FTP at ftp://ftp.genetics.wustl.edu/pub/eddy/software/forester.tar.Z
Contact: eddy@genetics.wustl.edu
Crystal structure of Staphylococcus aureus tyrosyl‐tRNA synthetase in complex with a class of potent and specific inhibitors
Authors: Qiu Xiayang , Janson Cheryl A. , Smith Ward W. , Green Susan M. , McDevitt Patrick , Johanson Kyung , Carter Paul , Hibbs Martin , Lewis Ceri , Chalker Alison , Fosberry Andrew , Lalonde Judith , Berge John , Brown Pamela , Houge‐Frydrych Catherine S.V. , Jarvest Richard L. 
Published: July 2002

AbstractSB‐219383 and its analogues are a class of potent and specific inhibitors of bacterial tyrosyl‐tRNA synthetases. Crystal structures of these inhibitors have been solved in complex with the tyrosyl‐tRNA synthetase from Staphylococcus aureus, the bacterium that is largely responsible for hospital‐acquired infections. The full‐length enzyme yielded crystals that diffracted to 2.8 Å resolution, but a truncated version of the enzyme allowed the resolution to be extended to 2.2 Å. These inhibitors not only occupy the known substrate binding sites in unique ways, but also reveal a butyl binding pocket. It was reported that the Bacillus stearothermophilus TyrRS T51P mutant has much increased catalytic activity. The S. aureus enzyme happens to have a proline at position 51. Therefore, our structures may contribute to the understanding of the catalytic mechanism and provide the structural basis for designing novel antimicrobial agents.
Lack of synergy for inhibitors targeting a multi‐drug‐resistant HIV‐1 protease
Authors: King Nancy M. , Melnick Laurence , Prabu‐Jeyabalan Moses , Nalivaika Ellen A. , Yang Shiow‐Shong , Gao Yun , Nie Xiaoyi , Zepp Charles , Heefner Donald L. , Schiffer Celia A. 
Published: July 2002

AbstractThe three‐dimensional structures of indinavir and three newly synthesized indinavir analogs in complex with a multi‐drug‐resistant variant (L63P, V82T, I84V) of HIV‐1 protease were determined to ∼2.2 Åresolution. Two of the three analogs have only a single modification of indinavir, and their binding affinities to the variant HIV‐1 protease are enhanced over that of indinavir. However, when both modifications were combined into a single compound, the binding affinity to the protease variant was reduced. On close examination, the structural rearrangements in the protease that occur in the tightest binding inhibitor complex are mutually exclusive with the structural rearrangements seen in the second tightest inhibitor complex. This occurs as adaptations in the S1 pocket of one monomer propagate through the dimer and affect the conformation of the S1 loop near P81 of the other monomer. Therefore, structural rearrangements that occur within the protease when it binds to an inhibitor with a single modification must be accounted for in the design of inhibitors with multiple modifications. This consideration is necessary to develop inhibitors that bind sufficiently tightly to drug‐resistant variants of HIV‐1 protease to potentially become the next generation of therapeutic agents.
Arcadia, Egypt
Authors: Palme Bernhard 
Published: December 2022

Abstract

Arcadia is the name of one of the Roman provinces located in Egypt in Late Antiquity. Created not long before 398
ce
, Arcadia's territory encompassed Middle Egypt from the top of the Nile Delta at Memphis to the border of the Thebaid near Hermopolis. Oxyrhynchos, the capital of Arcadia, and other major towns like Herakleopolis and Arsinoiton Polis are the main sites of papyrus finds. Consequently, Arcadia is among the best documented areas of the later Roman Empire. After the Arab conquest of Egypt in 640/1, Arcadia remained an administrative unit well into the eighth century.
Kingship, Hellenistic
Authors: Hannestad Lise 
Published: December 2022

AbstractIn the Greek world, the period from the death of Alexander (323bce) to the Roman conquest of Egypt (31bce) was characterized by the formation of a number of kingdoms. Alexander's senior officers immediately began fighting for power and land. Three large kingdoms and gradually a number of smaller ones were established that dominated the Greek world until 31bce.
Leukas (Leucas)
Authors: Bonelou Elena 
Published: December 2022

Abstract

Leukas (Leucas) is an island situated opposite northwestern Akarnania. Its name derives from the hero Leukadios, son of Ikarios, and the cape Leukata, at the southern part of the island. During the reign of the tyrant Kypselos, the Corinthians established a colony on the northeastern part of the island and opened the narrow channel between Leukas and Akarnania (
dioryktos
) to be navigable.
Intermolecular Cross‐Linking Reinforces Polymer Binders for Durable Alloy‐Type Anode Materials of Sodium‐Ion Batteries
Authors: Yao Qian , Zhu Yansong , Zheng Cheng , Wang Nana , Wang Dongdong , Tian Fang , Bai Zhongchao , Yang Jian , Qian Yitai , Dou Shixue 
Published: December 2022

AbstractSodium‐ion batteries show promising potential for large‐scale energy storage. However, the large size and heavy mass of Na+ always results in huge volume change and inferior electrochemical stability, especially in alloy‐type anode materials. Here, molecular engineering of the polymer binders, i.e., cross‐linking of poly(acrylic acid) with glycerin (PAA‐GLY), reinforces the mechanical properties, eliminates the active protons of PAA, and benefits electrolyte diffusion, thereby remarkably improving electrochemical performance. Using µ‐Sn as an example, the cycle life at 2 A g−1 is extended from ≈26 cycles of PAA to ≈2000 cycles of PAA‐GLY. Meanwhile, the initial Coulombic efficiency is promoted to 90.3%, allowing the fabrication step of electrode presodiation for full cells to be eliminated. Thus, the full cells run 300 cycles at 2 A g−1. In addition, the binder allows the thick electrode to exhibit an areal capacity of 6.8 mAh cm−2. This binder is also applied for µ‐Bi and µ‐Sb. The simple operation, remarkable improvement, and wide applications indicate the promising prospects of this strategy for advanced electrodes in sodium ion batteries.
SHORT syndrome with microcephaly and developmental delay
Authors: Patel Viraj , Cui Wei , Cobben Jan M. 
Published: December 2022

AbstractWe report a boy with typical clinical features of SHORT syndrome alongside a significant microcephaly and severe developmental delay associated with a de novo single nucleotide missense DNA variant resulting in a single amino acid change in codon 486 of the PIK3R1 gene (PIK3R1 c.1456G>A (p.Ala486Thr)). Our report strikingly coincides with another recently published case from Brazil, describing a 23‐year‐old woman with the same de novo PIK3R1 DNA variant, who also exhibits SHORT syndrome with severe secondary microcephaly and intellectual disability. On review of the literature, we have identified further cases of PIK3R1‐related SHORT Syndrome with a similar phenotype. We note all these cases (including ours) have variants located in the ‐inter SH2 domain (iSH2); we speculate that pathogenic iSH2 located PIK3R1 variants are associated with a different and otherwise unreported clinical picture of SHORT syndrome that presents with microcephaly and/or significant developmental delay/intellectual disability. The pathogenic mechanism of why these variants apparently lead to a different clinical picture of SHORT syndrome remains unknown.
Large and Robust Exchange Bias in Co/CoO film: Implication for Flexible Spintronics
Authors: Sun Yuting , Tang Wei , Chen Siliang , Liu Liang , Liu Haoliang , Ge Jun‐Yi , Zhang Xi , Jiang Wei‐Chao , Liang Huawei , Zeng Yu‐Jia 
Published: December 2022

AbstractDeveloping a robust and flexible exchange bias (EB) system is crucial for wearable spintronic devices. In this work, large and robust EB effect is demonstrated in flexible Co/CoO thin films grown by magnetron sputtering. The obtained EB field is as large as 6172 Oe at low temperatures on a flexible substrate. Based on the atomistic spin models, the unexpectedly large EB field is explained by the decrease of ferromagnetic grain size and the increase of ferromagnetic /antiferromagnetic contact area. Furthermore, the strain‐dependent coercivity and EB effect are observed in flexible Co/CoO films. Finally, the flexible Co/CoO thin film shows no degradation (even a slight increase) of performances in all figures of merit after 500 bending cycles, indicating excellent mechanical durability. This study sheds light on Co/CoO as a robust EB material for flexible spintronics.
Relatedness and compatibility: The concept of privacy in Mandarin Chinese and American English corpora
Authors: Ma Yuanye 
Published: December 2022

AbstractThis study investigates how privacy as an ethical concept exists in two languages: Mandarin Chinese and American English. The exploration relies on two genres of corpora from 10 years: social media posts and news articles, 2010–2019. A mixed‐methods approach combining structural topic modeling (STM) and human interpretation were used to work with the data. Findings show various privacy‐related topics across the two languages. Moreover, some of these different topics revealed fundamental incompatibilities for understanding privacy across these two languages. In other words, some of the variations of topics do not just reflect contextual differences; they reveal how the two languages value privacy in different ways that can relate back to the society's ethical tradition. This study is one of the first empirically grounded intercultural explorations of the concept of privacy. It has shown that natural language is promising to operationalize intercultural and comparative privacy research, and it provides an examination of the concept as it is understood in these two languages.
η6‐Metalated Aryl Iodides in Diels‐Alder Cycloaddition Reactions: Mode of Activation and Catalysis
Authors: Portela Susana , Fernández Israel 
Published: December 2022

AbstractThe potential application of η6‐metalated aryl iodides as organocatalyst has been explored by means of computational methods. It is found that the enhanced halogen bonding donor ability of these species, in comparison with their demetalated counterparts, translates into a significant acceleration of the Diels‐Alder cycloaddition reaction involving cyclohexadiene and methyl vinyl ketone. The factors behind this acceleration, theendo‐exoselectivity of the process and the influence of the nature of the transition metal fragment in the activity of these species are quantitatively explored in detail by means of the combination of the Activation Strain Model of reaction and the Energy Decomposition Analysis methods.
Understanding and Mitigating Interpersonal Communication Conflict in Field‐Based Institutions
Authors: McDermott Victoria , Kauten Rebecca , Gee Jennifer , May Amy 
Published: December 2022

AbstractInterpersonal communication conflict is an inevitable part of field‐based experiences due to the many complex variables that influence human interactions, such as culture, gender, and perceived power. Moreover, in field‐based institutions (i.e., field stations and marine laboratories) privacy may be limited in terms of space and time, and physical conditions may be challenging, which can lead to more frequent and intense interpersonal conflicts. Conflicts can arise episodically or cyclically at a field‐based institution, impacting visitors and employees at all levels, that is, between students, staff, faculty, and leadership. Those who work seasonally or permanently at field‐based institutions may be able to mitigate some of the potential negative outcomes associated with unmanaged conflict by knowing when these incidents might occur, as well as how to employ meaningful conflict management strategies during these times. Thus, we propose the 10/60 model of field station experiences to define significant points of time during a field experience in which collecting feedback may be critical for avoiding communication conflict. We provide additional recommendations on best practices for soliciting feedback, as well as the importance of setting explicit communication expectations for those in leadership positions to create more inclusive and equitable spaces.
Recurrence with lymph node and brain metastasis of an oncocytic carcinoma of the submandibular gland: A case report
Authors: Nechi Salwa , Gharbi Ghada , Douggaz Amel , Belfekih Houda , Chaabane Abir , Mfarrej Mohamed Karim , Chelbi Emna 
Published: December 2022

AbstractOncocytic carcinomas of the salivary glands are rare. The submandibular gland is a rare location. It is usually associated with a poor prognosis and recurrence after treatment. We report a case of a 52‐year‐old man with a lymph node and brain metastasis recurrence of an oncocytic carcinoma of the submandibular gland.
Emergent balloon pulmonary angioplasty in a patient with central‐type chronic thromboembolic pulmonary hypertension with cardiac shock
Authors: Tamura Hiroto , Hosokawa Shinobu , Yuba Kenichiro 
Published: December 2022

AbstractThe standard treatment of chronic thromboembolic pulmonary hypertension (CTEPH) is pulmonary endarterectomy (PEA); however, it may be unsuitable in the presence of comorbidities such as cardiac shock and severe hypoxia. We describe a successful case of emergent balloon pulmonary angioplasty performed before PEA in a patient with deteriorating central‐type CTEPH.
The Discovery of Imine Reductases and their Utilisation for the Synthesis of Tetrahydroisoquinolines
Authors: Cárdenas‐Fernández Max , Roddan Rebecca , Carter Eve M. , Hailes Helen C. , Ward John M. 
Published: December 2022

AbstractImine reductases (IREDs) are NADPH‐dependent enzymes with significant biocatalytic potential for the synthesis of primary, secondary, and tertiary chiral amines. Their applications include the reduction of cyclic imines and the reductive amination of prochiral ketones. In this study, twenty‐nine novel IREDs were revealed through genome mining. Imine reductase activities were screened at pH 7 and 9 and in presence of either NADPH or NADH; some IREDs showed good activities at both pHs and were able to accept both cofactors. IREDs with Asn and Glu at the key 187 residue showed preference for NADH. IREDs were also screened against a series of dihydroisoquinolines to synthesise tetrahydroisoquinolines (THIQs), bioactive alkaloids with a wide range of therapeutic properties. Selected IREDs showed high stereoselectivity, as well high THIQ yields (>90 %) when coupled to a glucose‐6‐phosphate dehydrogenase for NADPH cofactor recycling.
Temozolomide treatment inhibits spontaneous motivation for exploring a complex object in mice: A potential role of adult hippocampal neurogenesis in “curiosity”
Authors: Mañas‐Padilla M. Carmen , Melgar‐Locatelli Sonia , Vicente Lucía , Gil‐Rodríguez Sara , Rivera Patricia , Rodríguez‐Pérez Celia , Castilla‐Ortega Estela 
Published: December 2022

AbstractIntrinsic exploratory biases are an innate motivation for exploring certain types of stimuli or environments over others, and they may be associated with cognitive, emotional, and even personality‐like traits. However, their neurobiological basis has been scarcely investigated. Considering the involvement of the hippocampus in novelty recognition and in spatial and pattern separation tasks, this work researched the role of adult hippocampal neurogenesis (AHN) in intrinsic exploratory bias for a perceptually complex object in mice. Spontaneous object preference tasks revealed that both male and female C57BL/6J mice showed a consistent unconditioned preference for exploring “complex”—irregular—objects over simpler ones. Furthermore, increasing objects’ complexity resulted in an augmented time of object exploration. In a different experiment, male mice received either vehicle or the DNA alkylating agent temozolomide (TMZ) for 4 weeks, a pharmacological treatment that reduced AHN as evidenced by immunohistochemistry. After assessment in a behavioral test battery, the TMZ‐treated mice did not show any alterations in general exploratory and anxiety‐like responses. However, when tested in the spontaneous object preference task, the TMZ‐treated mice did not display enhanced exploration of the complex object, as evidenced both by a reduced exploration time—specifically for the complex object—and a lack of preference for the complex object over the simple one. This study supports a novel role of AHN in intrinsic exploratory bias for perceptual complexity. Moreover, the spontaneous complex object preference task as a rodent model of “curiosity” is discussed.
A Colloidal Synthesis Route Towards AgBiS2 Nanocrystals Based on Metal Xanthate Precursors
Authors: Vakalopoulou Efthymia , Knez Daniel , Sigl Marco , Kothleitner Gerald , Trimmel Gregor , Rath Thomas 
Published: December 2022

AbstractSilver bismuth sulfide (AgBiS2) is showing impressive thermoelectric and photovoltaic properties and has a high potential to replace toxic cadmium or lead containing semiconductors in many applications. Herein, we report on a synthesis route for AgBiS2 nanocrystals applying metal xanthates as precursors. Silver xanthates could not be used so far in solution‐based syntheses for Ag‐containing metal sulfide nanocrystals as they are typically insoluble in organic solvents. An investigation of the synthesis process revealed that even though the silver xanthate is not soluble in the used solvent mixture consisting of octadecene and oleylamine, the decomposition of both precursors and the formation of AgBiS2 nanocrystals is initiated already at room temperature by the amine functionality of the ligand. At room temperature, primary crystallite sizes of approximately 4 nm are observed and at a reaction temperature of 200 °C, the size of the AgBiS2 nanocrystals increases to 7–8 nm.
Synthesis of Highly Dispersible Functionalized Carbon Nanotubes as Conductive Material through a Facile Drying Process for High‐Power Lithium‐ion Batteries
Authors: Kim Jiseong , Park Da‐Bin , Hong Choi Jae , Jo Minki , Kim Seokhui , Oh Pilgun , Son Yoonkook 
Published: December 2022

AbstractHerein, surface‐functionalized carbon nanotubes (CNTs) were successfully synthesized by dry ball milling that facilitates industrial application. The optimal conditions were determined by analyzing the physicochemical characteristics of CNTs, including the content of the carboxyl group (−COOH) induced on the surface of CNTs by co‐existing dry ice based on the ball milling time. Among them, 30 s ball milling (CNTs‐30s) showed a high dispersibility in N‐methyl‐2‐pyrrolidone (NMP) while retaining most carboxyl groups and maintaining the intrinsic high conductivity. In the evaluation of rate capability and 5 C/5 C cyclability applied to the Li1+x(Ni1−y−zCoyMnz)1−xO2 with 60 % Ni (NCM622) cathode, CNTs‐30s showed excellent performance based on a well‐formed conductive network. Regarding improved dispersion properties and electrochemical performance, the optimal surface functionalization conditions, dispersibility, and electrode properties according to the processing time were analyzed; based on these, the correlation with electrochemical performance was confirmed.