bluuebunny/crossref_metadata_2025_split huggingface dataset:
HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy
Authors: Antunes Dinler A. , Abella Jayvee R. , Hall-Swan Sarah , Devaurs Didier , Conev Anja , Moll Mark , Lizée Gregory , Kavraki Lydia E. 
Published: July 2020

PURPOSEHLA protein receptors play a key role in cellular immunity. They bind intracellular peptides and display them for recognition by T-cell lymphocytes. Because T-cell activation is partially driven by structural features of these peptide-HLA complexes, their structural modeling and analysis are becoming central components of cancer immunotherapy projects. Unfortunately, this kind of analysis is limited by the small number of experimentally determined structures of peptide-HLA complexes. Overcoming this limitation requires developing novel computational methods to model and analyze peptide-HLA structures.METHODSHere we describe a new platform for the structural modeling and analysis of peptide-HLA complexes, called HLA-Arena, which we have implemented using Jupyter Notebook and Docker. It is a customizable environment that facilitates the use of computational tools, such as APE-Gen and DINC, which we have previously applied to peptide-HLA complexes. By integrating other commonly used tools, such as MODELLER and MHCflurry, this environment includes support for diverse tasks in structural modeling, analysis, and visualization.RESULTSTo illustrate the capabilities of HLA-Arena, we describe 3 example workflows applied to peptide-HLA complexes. Leveraging the strengths of our tools, DINC and APE-Gen, the first 2 workflows show how to perform geometry prediction for peptide-HLA complexes and structure-based binding prediction, respectively. The third workflow presents an example of large-scale virtual screening of peptides for multiple HLA alleles.CONCLUSIONThese workflows illustrate the potential benefits of HLA-Arena for the structural modeling and analysis of peptide-HLA complexes. Because HLA-Arena can easily be integrated within larger computational pipelines, we expect its potential impact to vastly increase. For instance, it could be used to conduct structural analyses for personalized cancer immunotherapy, neoantigen discovery, or vaccine development.
Assessing Genitourinary Cancer Clinical Trial Accrual Sufficiency Using Archived Trial Data
Authors: Stensland Kristian , Kaffenberger Samuel , Canes David , Galsky Matthew , Skolarus Ted , Moinzadeh Alireza 
Published: July 2020

PURPOSE Clinical trials often fail to reach their anticipated end points, most frequently because of poor accrual. Prior studies have analyzed trial termination, but it has not been easy to assess accrual estimates using international databases such as ClinicalTrials.gov because of limitations in accessing accrual information. Specifically, it is not easy to extract both anticipated and actual accrual of clinical trials. We designed a new algorithmic approach to extracting trial accrual data from ClinicalTrials.gov and used it to estimate the sufficiency of patient accrual onto genitourinary (GU) cancer trials. METHODS We queried ClinicalTrials.gov for completed/terminated phase II and III clinical trials for prostate, bladder, kidney, testicular, and ureteral cancers registered after 2007. We extracted trial characteristics from available XML files. We then used a Python algorithm to access prior trial registrations on the ClinicalTrials.gov archive site and extract both anticipated and actual accrual numbers. We then compared the actual accrual of each trial to its anticipated accrual and defined sufficient accrual as 85% of anticipated accrual. RESULTS The algorithm was 100% accurate compared with hand extraction in a small validation subset. A total of 925 trials were included, of which 840 (91%) had both anticipated and actual accrual. Only 418 (50%) trials had sufficient accrual (≥ 85% of anticipated). Considering only trials marked as successfully completed, 395/597 (66%) reached sufficient accrual. CONCLUSION GU cancer trials often do not meet their anticipated accrual goals. New approaches to trial conduct are direly needed. Our reproducible and scalable approach to extracting accrual information can be applied to analysis of ClinicalTrials.gov in future analyses in the hope of improving the efficiency of the clinical trials enterprise.
Rola języka w uwalnianiu się z dziedzicznych traum
Authors: Marcol Katarzyna 
Published: July 2020

The Role of Language in Releasing from Inherited Traumas. Negotiations of the Social Position of the Silesian Minority in Serbian Banat
The aim of the paper is to show the dependence between language, collective memory (also post-memory) and sense of identity. This issue is analysed using the example of an ethnic minority living in the village of Ostojićevo (Banat, Serbia) called ‘Toutowie.’ Their ancestors came in the 19th century from Wisła (Silesian Cieszyn, Poland); they left their homes because of great hunger and were looking for jobs in Banat. Narratives about the past contain traumatic experiences of the past generations transmitted in the Silesian dialect and constituting communicative memory. At the same time, a new Polish national identity is being constructed, supported by institutions and authorities; it carries a new image of the world and creates a new cultural memory. This new identity – shaped on the basis of national categories – leads to changes of its self-identification and gives the opportunity to raise its social position in the multi-ethnic Banat community.
Urynkowione znaki pamięci
Authors: Doległo Sławomir 
Published: July 2020

Commodified Memory Emblems. Historical Culture in the (Post)Consumptional Culture
Postmodernist consumption, developed by the order of self-realisation, increasingly shapes current historical awareness. Consequently, contemporary collective memory is composed not of dates and historical facts but of visual identification, slogans and varied communicative practices, so the components of popular brands which stimulate people’s consumable attitudes. The symbols of the Polish Resistance Movement during World War II as well as national colours and emblem move from historical and commemorative sphere to the sphere of pop culture. They commonly appear on T-shirts, tattoos, murals, social media profiles and political banners and are used to clarify the present day through the prism of the past, to articulate people’s ideas, concerns and affinities. The ‘language’ of memory boom surprisingly corresponds to the rhetoric of present global cultural industry, which is the ‘natural environment’ of communication for Millennials and Post-Millennials. The article is an attempt to summarise the most influential academic perspectives of current memory culture, dominated by media and consumable practices.
Os processos de circulação do Caso Pablo Katchadjian
Authors: Amâncio Nair Renata 
Published: July 2020

Apresentaremos o conceito de Objetos Derivados e a sua pertinência para pensar os processos de circulação do livro El Aleph Engordado (2009). O conceito é fruto da pesquisa A rasura da autoria na literatura contemporânea: O caso Pablo Katchadjian (Processo FAPESP: nº2017/25218-0) na qual construímos uma proposta de leitura para os objetos (#Yoborges, Reality Avoider e Apoyo a Pablo Katchadjian) que surgiram por consequência da publicação do livro El Alpeh Engordado (2009) que fez uso do conto El Aleph (1949) do celebre Jorge Luís Borges (1986). Discutiremos o Caso Pablo Katchadjian dando ênfase em seus objetos derivados e colocando em questão novas possibilidades de compreensão para a autoria no tempo presente.
My Chief Interest Is Germination: an Interview with Elisa Kay Sparks
Authors: Sparks Elisa Kay , Santos Brigida Marcela , Sant’Ana Ferreira Mendes Thales 
Published: July 2020

Elisa Kay Sparks, Professor Emerita of English at Clemson University, has established a career that is a source of inspiration to any scholar in the Humanities. Having taught Literature and Women’s Studies for 35 years at Clemson, she is part of the history of entire generations of students. Furthermore, Professor Sparks's research interests and practices put her at an ideal standpoint to discuss the “connections and innovations” element of this number's theme. She is an international reference in Virginia Woolf and Modernist Studies and one of the Virginia Woolf International Society’s main collaborators. Throughout the years, she has established an impressive body of critical work investigating parks, gardens, and flowers in Woolf’s life and writing. She has also drawn innovative connections between the works of the modernist writer and those of the American painter Georgia O’Keeffe. Taking in the stature of Professor Sparks’s contributions to Woolf Studies specifically and to the Humanities in a broader sense allows us to fully appreciate the reach of her views on the importance of sharing knowledge. For, beyond the fact that Professor Sparks is a prolific researcher, she is a truly generous one. Throughout the years, she has authored numerous blogs sharing her findings with readers and researchers entirely for free. In this interview, it becomes clear that, allied with the rigour of her academic production and her extraordinary career as a teacher, this impulse towards making knowledge and critical thinking as widely available as possible makes Professor Sparks a model of academic practice we should all aspire to.
Salud laboral desde los servicios de la administración sanitaria: las oportunidades de la “perspectiva laboral” para el ejercicio de la salud pública
Authors: García García Ana María 
Published: July 2020

La interacción entre salud pública y salud laboral desde los correspondientes servicios de la administración sanitaria sigue un abordaje que se podría formular en los siguientes términos: ¿qué puede hacer la salud pública por el mejor ejercicio la salud laboral?. Así, en salud laboral se trasladan a la atención sobre la población trabajadora conceptos y herramientas propios de la salud pública tales como los sistemas de vigilancia de enfermedades o los programas de promoción de la salud que, pese a las mutilaciones que impone “la puerta de la fábrica”, contribuyen a proteger y mejorar la salud de la población trabajadora. También se apuntan con enorme potencial (y no pocas dificultades) propuestas más recientes para prevenir y actuar sobre la violencia de género desde el medio laboral o para incorporar el principio de “salud en todas las políticas” en las decisiones organizativas de la empresa. Ese espejo de las prioridades y focos de la salud pública en el ejercicio de la salud laboral ha enriquecido y seguirá enriqueciendo a esta última, aportando estrategias y nuevas oportunidades para la acción. Pero en este Editorial planteamos una perspectiva complementaria y creemos que escasamente explorada en nuestro ámbito (tampoco muy presente en la bibliografía internacional) y que respondería al siguiente planteamiento: ¿qué puede hacer la salud laboral por el mejor ejercicio de la salud pública?…
Harmonic and rational harmonic driving of microresonator soliton frequency combs
Authors: Xu Yiqing , Lin Yi , Nielsen Alexander , Hendry Ian , Coen Stéphane , Erkintalo Miro , Ma Huilian , Murdoch Stuart G. 
Published: July 2020

With demonstrated applications ranging from metrology to
telecommunications, soliton microresonator frequency combs have
emerged over the past decade as a remarkable new technology. However,
standard implementations allow only for the generation of combs whose
repetition rate is tied closely to the fundamental resonator
free-spectral range (FSR), offering little or no dynamic control over
the comb line spacing. Here we propose and experimentally demonstrate
harmonic and rational harmonic driving as novel techniques that allow
for the robust generation of soliton frequency combs with discretely
adjustable frequency spacing. By driving an integrated Kerr
microresonator with a periodic train of picosecond pulses whose
repetition rate is set close to an integer harmonic of the 3.23 GHz
cavity FSR, we deterministically generate soliton frequency combs with
frequency spacings discretely adjustable between 3.23 GHz and
19.38 GHz. More remarkably, we also demonstrate that driving the
resonator at rational fractions of the FSR allows for the generation
of combs whose frequency spacing corresponds to an integer harmonic of
the pump repetition rate. By measuring the combs’ radio-frequency
spectrum, we confirm operation in the low-noise soliton regime with no
supermode noise. The novel techniques demonstrated in our work provide
new degrees of freedom for the design of synchronously pumped soliton
frequency combs.
Common-clock very long baseline interferometry using a coherent optical fiber link
Authors: Clivati Cecilia , Aiello Roberto , Bianco Giuseppe , Bortolotti Claudio , De Natale Paolo , Di Sarno Valentina , Maddaloni Pasquale , Maccaferri Giuseppe , Mura Alberto , Negusini Monia , Levi Filippo , Perini Federico , Ricci Roberto , Roma Mauro , Santamaria Amato Luigi , Siciliani de Cumis Mario , Stagni Matteo , Tuozzi Alberto , Calonico Davide 
Published: July 2020

Among the most powerful techniques for the exploration of the Universe is very long baseline interferometry (VLBI), which is based on the simultaneous observation of radio sources in the sky with arrays of distant ground-based antennas. One of the effects currently limiting its ultimate sensitivity is the phase-instability of the reference clocks adopted at each antenna. This term can be made negligible delivering the same clock signal to multiple telescope sites using optical fibers. We realized such an infrastructure by disseminating a coherent optical frequency signal to two distant radio telescopes using a 1739-km-long fiber. We performed a 24 h geodetic VLBI campaign in which the same clock reference was used at both telescopes and analyzed it using standard VLBI procedures. The results were consistent with the expectations, confirming that the proposed approach is feasible and configures as a novel tool for studying the role of clocks, troposphere, and systematic effects in the ultimate VLBI resolution.
Kehadiran Gelombang Soliter dan Transpor Sesaat Sedimen tersuspensi di Perairan Pantai Bengkulu Tengah
Authors: Kusmanto Edi , Hasanudin Muhammad 
Published: July 2020

<strong>Existence of Solitary Waves and Transient Suspended Sediment Transport in the Coastal Waters of Central Bengkulu. </strong>Coastal abrasion and suspended sediment transport driven by waves is occurring dreadfully in the coastal waters of Central Bengkulu. The abrasion tends to be accelerated by solitary waves during the southeast monsoon season. The primary data were obtained on 17-26 July 2014, while the secondary data derived from Google Maps imageries obtained on 17 June 2014, representing the southeast monsoon season. The primary data were collected by 1200 KHz Acoustic Doppler Current Profiler (ADCP) for water currents, a single beam Echosounder for depths, Garmin 276C GPS receiver for coordinate positions, RBR-TWR2050 (installed at at a fixed point at 102.2219 °E and 3.6916 °S and depth of 9 m) for height and wave periods, and a compass for the direction of wave propagation. The secondary data included Astrium satellite imageries compiled by Google Earth and displayed as Google Maps images on 17 June 2014. These images were used for identifying the appearance of wave groups and by using a feature in Google Earth, it showed that the estimated distance between wave packets hitting the coast accounted for 147 m. This study showed the existence of solitary waves with height and wave period of 1.02 m and 13.85 seconds respectively, while the wave length reached 147.7 m. The wave energy and wave energy flux were 1123.12 Jm<sup>-2</sup> and 12018.94 Jm<sup>-1</sup>s<sup>-1</sup>, calculated by using the cnoidal wave theory and solved by the KdV equation. These solitary waves have large destructive forces on unstable cliffs along the coasts. Derived from coastal abrasion processes and shown by the ADCP backscatter intensity with the highest of 146 dB, the suspended sediments were likely to be transported by water currents with an average speed of 25.99 cm s<sup>-1</sup> in the dominant direction to the south - southeast; and the sediments were deposited along the coast of Bengkulu City.
Islam and Local Traditions: The Study of the Thinkings of Abdurrahman Wahid (1940-2009) and Khalil Abdul Karim (1930-2002) an Indonesian and an Egyptian Perspective
Authors: Mahmudah Siti 
Published: July 2020

Islam and local tradition had already coexisted peacefully since Islam was revealed by Allah for the first time through the Gabriel Angel to the Prophet Muhammad in Mecca on 610 M. According to Mohammed A. Muqtedar Khan, there were traditions and ethics of Islam, based on the origin of the the sharia misunderstood by the most Muslims until now. Abdurrahman Wahid (Gus Dur) with his theory of the Pribumisasi Islam and Khalil Abdul Karim with his theory about the early existence of the Islam and sharia has been revealed among the pre-Islamic Arab tradition as the blueprint for Islam and the sharia in this era. Both of these theories are those of the continuation of Islam for all times and places. For the first time, Islam and the sharia gave high appreciation and respect to the Arab tradition and had even enshrined Arab traditions that are considered good and maslahat for humanitarian life remains entrenched to the teachings of Islam and enshrined in the Qur'an. Both of these theories can be used as the basis for rejecting the discovery of Timothy Daniel about "Islamic Spectrum in Java" (2009) which holds that the religious practice of Java is the Kejawen belief (a syncretic), because the teachings of Islam has mixed with local traditions. Therefore, I assert that the religious practice of Java is very diverse and cannot be called as a Kejawen belief (a syncretic). The practice of the Kejawen belief in religious practice in Java is a form of Islam whichis a contextual learning and will continue its process on the perfection of Islam to continue to honor the tradition of the Javanese community that has been practiced by their ancestors and has been successively crystallized and is very difficult to eliminate. Some examples are: bathing with flower tradition in the wedding event, laying flowers at the entrance of the house every Friday night, and riyungan. The reason is that the Muslim community is still able to practice the good and maslahat tradition like in the first era ofIslam in Mecca and Madina.
Le terme ẖnw et le début du Naufragé
Authors: Obsomer Claude 
Published: July 2020

Le terme ẖnw est attesté à quatorze reprises dans le récit du Naufragé : 7 fois dans la préposition composée m-ẖnw, 7 fois en tant que substantif. Rares sont les traducteurs de l'oeuvre qui ont traduit de la même manière les 7 occurrences du nom ẖnw : Résidence, pays, patrie, … Cette hésitation sur le sens à lui conférer concerne surtout la première occurrence du terme, lorsque le bateau arrive à quai au terme de l'expédition de Nubie. Les marins sont-ils à Éléphantine, comme on l'a souvent cru, ou à la Résidence de Licht ? Cette étude permet de lever toute ambiguïté sur ce point important pour la compréhension de l'oeuvre. C'est au port de Licht que le bateau se trouve amarré de retour de Nubie.
Equivalence of Friction and Viscous Damping in a Spring-Friction System with Concave Friction Distribution
Authors: Li Shanshan , Wei Biao , Tan Hao , Li Chaobin , Zhao Xiaomiao 
Published: July 2020

Abstract
With the aim of unifying the damping concept and evaluating the amount of damping in a structure, this paper investigates whether friction action can be equivalent to traditional viscous damping. The research focused on purely concave friction distribution cases, uniform friction distribution cases, and their combination cases in a spring-friction isolation system. The dynamic responses of a numerical method using friction action were compared with those of another numerical methods using equivalent viscous damping under sine wave ground motions. The comparison of results shows that the friction action can be converted to the equivalent viscous damping action with some errors by using an equation. The conversion accuracy of uniform friction distribution cases using the first term of the equation is much worse than that of the purely concave friction distribution cases using the second term of the equation. The reason for this being that the uniform friction distribution can prevent the structure from sliding back to its center after the ground motion; however, the viscous damping action does not have such a negative function. The comparison errors, between using the friction action and using the equivalent viscous damping, are directly proportional to the ratio of the component of uniform friction distribution to the component of purely concave friction distribution.
Complex Interactions between Genes and Social Environment Cause Phenotypes Associated with Autism Spectrum Disorders in Mice
Authors: Sledziowska Monika , Kalbassi Shireene , Baudouin Stéphane J. 
Published: July 2020

AbstractThe etiology of autism spectrum disorders (ASDs) is a complex combination of genetic and environmental factors. Neuroligin3, a synaptic adhesion protein, and cytoplasmicFMR1interacting protein 1 (CYFIP1), a regulator of protein translation and actin polymerization, are two proteins associated with ASDs that interact in neuronsin vivo. Here, we investigated the role of the Neuroligin3/CYFIP1 pathway in behavioral functioning and synapse formation in mice and found that it contributes to motor learning and synapse formation in males. Similar investigation in female mice revealed an absence of such phenotypes, suggesting that females are protected against mutations affecting this pathway. Previously, we showed that the social environment influences the behavior of male mice. We extended this finding and found that the transcriptome of wild-type mice housed with their mutant littermates, lacking Neuroligin3, differed from the transcriptome of wild-type mice housed together. Altogether, these results identify the role of the Neuroligin3/CYFIP1 pathway in male mouse behavior and highlight its sensitivity to social environment.
Development of a Mouse Reporter Strain for the Purinergic P2X2Receptor
Authors: Kim Seol-Hee , Bahia Parmvir K. , Patil Mayur , Sutton Sydney , Sowells Isobel , Hadley Stephen H. , Kollarik Marian , Taylor-Clark Thomas E. 
Published: July 2020

AbstractThe ATP-sensitive P2X2ionotropic receptor plays a critical role in a number of signal processes including taste and hearing, carotid body detection of hypoxia, the exercise pressor reflex and sensory transduction of mechanical stimuli in the airways and bladder. Elucidation of the role of P2X2has been hindered by the lack of selective tools. In particular, detection of P2X2using established pharmacological and biochemical techniques yields dramatically different expression patterns, particularly in the peripheral and central nervous systems. Here, we have developed a knock-in P2X2-cre mouse, which we crossed with a cre-sensitive tdTomato reporter mouse to determine P2X2expression. P2X2was found in more than 80% of nodose vagal afferent neurons, but not in jugular vagal afferent neurons. Reporter expression correlated in vagal neurons with sensitivity to α,β methylene ATP (αβmATP). P2X2was expressed in 75% of petrosal afferents, but only 12% and 4% of dorsal root ganglia (DRG) and trigeminal afferents, respectively. P2X2expression was limited to very few cell types systemically. Together with the central terminals of P2X2-expressing afferents, reporter expression in the CNS was mainly found in brainstem neurons projecting mossy fibers to the cerebellum, with little expression in the hippocampus or cortex. The structure of peripheral terminals of P2X2-expressing afferents was demonstrated in the tongue (taste buds), carotid body, trachea and esophagus. P2X2was observed in hair cells and support cells in the cochlear, but not in spiral afferent neurons. This mouse strain provides a novel approach to the identification and manipulation of P2X2-expressing cell types.