bluuebunny/crossref_metadata_2025_split huggingface dataset:
Successful application of genome sequencing in a diagnostic setting: 1007 index cases from a clinically heterogeneous cohort
Authors: Bertoli-Avella Aida M. , Beetz Christian , Ameziane Najim , Rocha Maria Eugenia , Guatibonza Pilar , Pereira Catarina , Calvo Maria , Herrera-Ordonez Natalia , Segura-Castel Monica , Diego-Alvarez Dan , Zawada Michal , Kandaswamy Krishna K. , Werber Martin , Paknia Omid , Zielske Susan , Ugrinovski Dimitar , Warnack Gitte , Kampe Kapil , Iurașcu Marius-Ionuț , Cozma Claudia , Vogel Florian , Alhashem Amal , Hertecant Jozef , Al-Shamsi Aisha M. , Alswaid Abdulrahman Faiz , Eyaid Wafaa , Al Mutairi Fuad , Alfares Ahmed , Albalwi Mohammed A. , Alfadhel Majid , Al-Sannaa Nouriya Abbas , Reardon Willie , Alanay Yasemin , Rolfs Arndt , Bauer Peter 
Published: August 2020

AbstractDespite clear technical superiority of genome sequencing (GS) over other diagnostic methods such as exome sequencing (ES), few studies are available regarding the advantages of its clinical application. We analyzed 1007 consecutive index cases for whom GS was performed in a diagnostic setting over a 2-year period. We reported pathogenic and likely pathogenic (P/LP) variants that explain the patients’ phenotype in 212 of the 1007 cases (21.1%). In 245 additional cases (24.3%), a variant of unknown significance (VUS) related to the phenotype was reported. We especially investigated patients which had had ES with no genetic diagnosis (n = 358). For this group, GS diagnostic yield was 14.5% (52 patients with P/LP out of 358). GS should be especially indicated for ES-negative cases since up to 29.6% of them could benefit from GS testing (14.5% with P/LP,n = 52 and 15.1% with VUS,n = 54). Genetic diagnoses in most of the ES-negative/GS-positive cases were determined by technical superiority of GS, i.e., access to noncoding regions and more uniform coverage. Importantly, we reported 79 noncoding variants, of which, 41 variants were classified as P/LP. Interpretation of noncoding variants remains challenging, and in many cases, complementary methods based on direct enzyme assessment, biomarker testing and RNA analysis are needed for variant classification and diagnosis. We present the largest cohort of patients with GS performed in a clinical setting to date. The results of this study should direct the decision for GS as standard second-line, or even first-line stand-alone test.
Agar with embedded channels to study root growth
Authors: Aziz Azlan Abdul , Lim Kai Boon , Rahman Ena Kartina Abdul , Nurmawati Muhammad Hanafiah , Zuruzi Abu Samah 
Published: August 2020

AbstractAgar have long been used as a growth media for plants. Here, we made agar media with embedded fluidic channels to study the effect of exposure to nutrient solution on root growth and pull-out force. Black Eye bean (Vigna Unguiculata) and Mung bean (Vigna Radiata) were used in this study due to their rapid root development. Agar media were fabricated using casting process with removable cores to form channels which were subsequently filled with nutrient solution. Upon germination, beans were transplanted onto the agar media and allowed to grow. Pull-out force was determined at 96, 120 and 144 h after germination by applying a force on the hypocotyl above the gel surface. The effect of nutrients was investigated by comparing corresponding data obtained from control plants which have not been exposed to nutrient solution. Pull-out force of Black Eye bean plantlets grown in agar with nutrient solution in channels was greater than those grown in gel without nutrients and was 110% greater after 144 h of germination. Pull-out force of Mung bean plantlets grown in agar with and without nutrient solution was similar. Tap root lengths of Black Eye bean and Mung Bean plantlets grown in agar with nutrient solution are shorter than those grown without nutrient.
Unitary transformation for Poincaré beams on different parts of Poincaré sphere
Authors: Sun Xibo , Geng Yuanchao , Zhu Qihua , Huang Wanqing , Zhang Ying , Wang Wenyi , Liu Lanqin 
Published: August 2020

AbstractWe construct an experimental setup, consisting of conical refraction transformation in two biaxial cascade crystals and 4f-system, to realize Unitary transformation of light beam and the manipulation of Poincaré beams on the different parts of Poincaré sphere. The spatial structure of the polarization can be controlled by changing the polarization of the incident beam or rotating the angle between these two crystals. The beams with different SoPs covering the full-Poincaré sphere, part-Poincaré sphere and one point on the sphere are generated for the different angles between crystals. The Unitary transformation of light beam is proposed in the experiment with the invariant intensity distribution. Subsequently, the spin angular momentum is derived from the distribution of polarization measured in our experiment. Moreover, the conversion between orbital angular momentum and spin angular momentum of light beam is obtained by changing the angle between crystals. And the conversion progress can also be influenced by the polarization of incident beam. We realized the continuous control of the spatial structure of the angular momentum density, which has potential in the manipulation of optical trapping systems and polarization-multiplexed free-space optical communication.
Increasing incidence of acute autoimmune hepatitis: a nationwide survey in Japan
Authors: Takahashi Atsushi , Ohira Hiromasa , Abe Kazumichi , Zeniya Mikio , Abe Masanori , Arinaga-Hino Teruko , Torimura Takuji , Yoshizawa Kaname , Takaki Akinobu , Kang Jong-Hon , Suzuki Yoshiyuki , Nakamoto Nobuhiro , Inui Ayano , Tanaka Atsushi , Takikawa Hajime 
Published: August 2020

AbstractThe Japanese diagnostic guidelines for autoimmune hepatitis (AIH) were proposed in 2014. This study aimed to determine the trends and characteristics of AIH based on a Japanese nationwide survey. Data for 796 patients who were newly diagnosed with AIH from 2014 to 2017 were collected from January to March, 2019 from 54 hospitals throughout Japan. Clinical characteristics, including treatment, were compared with those reported in a prior 2015 survey. The population had a median age of 63 years at diagnosis, and the male to female ratio was 1:5.3. The numbers of women was significantly lower in this survey than in the 2015 survey. Moreover, the incidence of AIH with histological acute hepatitis increased significantly from 11.0 to 21.7%. The changes in the laboratory findings, such as in transaminase and immunoglobulin G levels and antinuclear antibody titers, as well as in prednisolone treatment, reflected an increasing incidence of acute AIH. The clinical characteristics of AIH changed rapidly, in parallel with the increasing incidence of acute AIH. The elucidation and diagnosis of AIH with acute hepatitis are important in the management of AIH.
Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching
Authors: Shendy Noha Ahmed Mohammed , Raghu Deepthi , Roy Sujoy , Perry Charles Hamilton , Safi Adiba , Branco Miguel Ramos , Homayouni Ramin , Abell Amy Noel 
Published: August 2020

AbstractCoordinated gene expression is required for phenotypic switching between epithelial and mesenchymal phenotypes during normal development and in disease states. Trophoblast stem (TS) cells undergo epithelial-mesenchymal transition (EMT) during implantation and placentation. Mechanisms coordinating gene expression during these processes are poorly understood. We have previously demonstrated that MAP3K4-regulated chromatin modifiers CBP and HDAC6 each regulate thousands of genes during EMT in TS cells. Here we show that CBP and HDAC6 coordinate expression of only 183 genes predicted to be critical regulators of phenotypic switching. The highest-ranking co-regulated gene is the NF-κB family member Rel. Although NF-κB is primarily regulated post-transcriptionally, CBP and HDAC6 control Rel transcript levels by binding Rel regulatory regions and controlling histone acetylation. REL re-expression in mesenchymal-like TS cells induces a mesenchymal-epithelial transition. Importantly, REL forms a feedback loop, blocking HDAC6 expression and nuclear localization. Together, our work defines a developmental program coordinating phenotypic switching.
Loss of β-cell identity and diabetic phenotype in mice caused by disruption of CNOT3-dependent mRNA deadenylation
Authors: Mostafa Dina , Yanagiya Akiko , Georgiadou Eleni , Wu Yibo , Stylianides Theodoros , Rutter Guy A. , Suzuki Toru , Yamamoto Tadashi 
Published: August 2020

AbstractPancreatic β-cells are responsible for production and secretion of insulin in response to increasing blood glucose levels. Defects in β-cell function lead to hyperglycemia and diabetes mellitus. Here, we show that CNOT3, a CCR4–NOT deadenylase complex subunit, is dysregulated in islets in diabetic db/db mice, and that it is essential for murine β cell maturation and identity. Mice with β cell-specific Cnot3 deletion (Cnot3βKO) exhibit impaired glucose tolerance, decreased β cell mass, and they gradually develop diabetes. Cnot3βKO islets display decreased expression of key regulators of β cell maturation and function. Moreover, they show an increase of progenitor cell markers, β cell-disallowed genes, and genes relevant to altered β cell function. Cnot3βKO islets exhibit altered deadenylation and increased mRNA stability, partly accounting for the increased expression of those genes. Together, these data reveal that CNOT3-mediated mRNA deadenylation and decay constitute previously unsuspected post-transcriptional mechanisms essential for β cell identity.
A Localized surface plasmon resonance (LSPR) sensor integrated automated microfluidic system for multiplex inflammatory biomarker detection
Authors: Chen Jhih-Siang , Chen Pin-Fan , Lin Hana Tzu-Han , Huang Nien-Tsu 
Published: August 2020

We integrated an LSPR sensor with a single-layer four-channel microfluidic device operated via the automated microfluidic control system to realize multiplex inflammatory biomarker detection.
DNVF-Memorandum Versorgungsforschung in der Onkologie
Authors: Kowalski Christoph , Albert Ute-Susann , Baumann Walter , Carl Ernst-Günther , Ernstmann Nicole , Hermes-Moll Kerstin , Fallenberg Eva Maria , Feick Günter , Feiten Stefan , Härter Martin , Heidt Vitali , Heuser Christian , Hübner Joachim , Joos Stefanie , Katalinic Alexander , Kempkens Özlem , Kerek-Bodden Hedy , Klinkhammer-Schalke Monika , Koller Michael , Langer Thomas , Lehner Burkhard , Lux Michael P. , Maatouk Imad , Pfaff Holger , Ratsch Boris , Schach Susanne , Scholl Isabelle , Skoetz Nicole , Voltz Raymond , Wiskemann Joachim , Inwald Elisabeth 
Published: August 2020

ZusammenfassungVersorgungsforschung in der Onkologie beschäftigt sich mit allen Situationen, in denen Menschen mit Krebs konfrontiert sind. Sie betrachtet die verschiedenen Phasen der Versorgung, also Prävention/Früherkennung, Prähabilitation, Diagnostik, Therapie, Rehabilitation und Palliativversorgung ebenso wie die verschiedenen Akteure, darunter die Betroffenen, die Versorgenden und die Selbsthilfe. Sie befasst sich mit Gesunden (z. B. im Rahmen von Prävention/ Früherkennung), Patientin-nen und Patienten und Krebs-Überlebenden. Aus den Besonderheiten von Krebserkrankungen und den etablierten Versorgungsstrukturen ergeben sich eine Reihe von inhaltlichen Spezifika für die Versorgungsforschung in der Onkologie im Vergleich zur allgemeinen Versorgungsforschung bei im Wesentlichen identischem Methodenkanon. Dieses Memorandum beschreibt den Gegenstand, illustriert die Versorgungsstrukturen und benennt Themenfelder der Versorgungsforschung in der Onkologie. Dieses Memorandum ist eine Ausarbeitung der Fachgruppe Onkologie des Deutschen Netzwerks Versorgungsforschung e. V. und Ergebnis intensiver Diskussionen.
Charakteristika von Diabetespatienten mit und ohne Pflegebedürftigkeit
Authors: Hodeck Katja , Tittel Sascha R. , Dreyhaupt Ines , Beer Renate , Petermann Sandy , Risse Alexander , Weyer Marc , Hake Kathrin , Schiel Ralf , Holl Reinhard W. 
Published: August 2020

ZusammenfassungIm Rahmen der vorliegenden multizentrischen Auswertung mit 6.424 Pflegepatienten unter 500.973 Menschen mit Diabetes aus dem DPV-Register wird die Erkrankungssituation der Pflegebedürftigen im Vergleich zu Patienten ohne Pflegebedürftigkeit, differenziert nach Altersgruppen und Diabetestyp, dargestellt.15 % der Pflegebedürftigen haben einen Typ-1-Diabetes, darunter fallen 99,0 % der Kinder, 9,5 % der 18- bis 75-Jährigen und 2,4 % der über 75-Jährigen. Pflegebedürftigkeit ist bei Erwachsenen und Senioren insbesondere mit den Krankheitsbildern Demenz, Depression, Herzinsuffizienz, Durchblutungsstörungen der Hirngefäße/Schlaganfall sowie mit dem diabetischen Fußsyndrom/Amputationen assoziiert. In der diabetologischen Therapie des Typ-2-DM wird bei 77 % der Pflegebedürftigen und damit deutlich häufiger als in der Vergleichsgruppe mit 55 % Insulin eingesetzt. Trotz höherer HbA1c-Werte und höherer Nüchternglukose als bei Typ-2-Patienten ohne Pflege treten unter Pflegebedürftigen gleichzeitig signifikant häufiger Hypoglykämien mit und ohne Koma auf. Stoffwechselbedingte Entgleisungen führten bei 15 % der Pflegepatienten mit Typ-2-DM gegenüber nur 6 % der Menschen mit Typ-2-DM ohne Pflegebedarf zu Klinikaufnahmen.Im Rahmen der Versorgung sollte verstärkt auf die Vermeidung von Stoffwechselentgleisungen geachtet und präventiv auf einen späteren Eintritt der assoziierten Krankheitsbilder hingewirkt werden. Die Versorgungsstrukturen sollten regional auf die Begleitung der Betroffenen spezialisiert werden. In der Aus- und Weiterbildung von Pflegepersonal und Ärzten sollten die Besonderheiten von jungen und alten Menschen mit Typ-1- und Typ-2-Diabetes stärker beachtet werden.
Positionspapier: Hinweise zur Patienteninformation und -aufklärung vor Anwendung von Biologika bei chronischer Rhinosinusitis mit Polyposis nasi (CRSwNP) – Empfehlungen des Ärzteverbandes Deutscher Allergologen (AeDA) und der Deutschen Gesellschaft für HNO-Heilkunde, Kopf- und Halschirurgie (DGHNOKHC) – Teil 1: Dupilumab
Authors: Klimek L. , Beule A. G. , Förster-Ruhrmann U. , Becker S. , Chaker A. , Huppertz T. , Hagemann J. , Hoffmann T. K. , Dazert S. , Deitmer T. , Wrede H. , Schlenter W. , Welkoborsky H. J. , Wollenberg B. , Olze H. , Rudack C. , Sperl A. , Casper I. , Dietz A. , Wagenmann M. , Zuberbier T. , Bergmann K. C. , Bedbrook A. , Bousquet J. , Bachert C. 
Published: August 2020

ZusammenfassungHintergrund Die chronische Rhinosinusitis mit Nasenpolypen (CRSwNP) ist eine multifaktorielle entzündliche Erkrankung der nasalen und paranasalen Schleimhaut, der oftmals eine Typ-2-Inflammation zugrunde liegt. Durch die Entwicklung von Biologika, die in diese Entzündungsmechanismen eingreifen können, steht eine neuartige Therapiemöglichkeit zur Verfügung.Methoden Auf Grundlage des aktuellen Wissensstandes zur Immunologie der CRSwNP und der Wirkung von Biologika sowie deren mögliche unerwünschte Wirkungen werden Empfehlungen für die Patienteninformation entwickelt.Ergebnisse Basierend auf der internationalen Literatur und bisherigen Erfahrungen hat ein Expertengremium Empfehlungen für die Patienteninformation und -aufklärung zur Anwendung von Biologika bei CRSwNP entwickelt und auf dieser Grundlage einen Aufklärungsbogen erstellt.Schlussfolgerung Die Information und Einwilligung des Patienten ist vor der Verordnung bzw. Verabreichung von Biologika erforderlich. Das vorliegende Positionspapier enthält wichtige Informationen hierzu und einen Vorschlag für eine Patienteninformation.
L-Asparaginase activity analysis, ansZ gene identification and anticancer activity of a new Bacillus subtilis isolated from sponges of the Red Sea
Authors: Ameen Fuad , Alshehri Wafa A , Al-Enazi Nouf M , Almansob Abobakr 
Published: August 2020

Abstract
This study describes the isolation of various marine bacteriafrom sponges collected from the Red Sea (Saudi Arabia) andL-asparaginase (anti-cancer enzyme) production from bacterialisolates. The 16S rDNA based phylogenetic analysis revealed thatthe isolate WSA3 was a Bacillus subtilis. Its partial-length genesequence was submitted to GenBank under the accession numberMK072695. The new B. subtilis strain harbored the exact size(1128 bp) of the new L-asparaginase (ansZ) gene as confirmedby PCR and in gel visualization, which was submitted to the NCBIdatabase (accession number MN566442). The molecular weightof partially purified L-asparaginase was determined as 45 kDa bySDS-PAGE. In addition, the enzyme L-asparaginase did not showglutaminase activity which is very important from a medical pointof view. Moreover, 100 μg/mL of the partially purified B. subtilis Lasparaginaseshowed promising anti-cancer activities when testedagainst three cancer cell lines (HCT-116, MCF-7, and HepG2).
Variational ansatz for p-wave fermions confined in a one-dimensional harmonic trap
Authors: Kościk Przemysław , Sowiński Tomasz 
Published: August 2020

Abstract
We propose a very accurate and efficient variational scheme for the ground state of the system of p-wave attractively interacting fermions confined in a one-dimensional harmonic trap. By the construction, the method takes the non-analytical part of interactions exactly into account and thus it approximates the true ground-state wave function in a whole range of interactions very accurately. Within the method, we determine different properties of the system for a different number of particles and different interactions. In this way, we explore how the system and its features transit from the ideal non-interacting Fermi gas to the system of infinitely strong attractions. Additionally, we demonstrate that the ansatz may also be used on a repulsive branch of interactions where other numerical methods break down. The presented method of including zero-range interactions is very universal and may be easily generalized to other one-dimensional confinements.
Invariant-mass distribution of top-quark pairs and top-quark mass determination *
Authors: Ju Wan-Li , Wang Guoxing , Wang Xing , Xu Xiaofeng , Xu Yongqi , Yang Li Lin 
Published: August 2020

Abstract
In this study, we investigate the invariant-mass distribution of top-quark pairs near the 2mt
threshold, which strongly influences the determination of the top-quark mass mt
. Higher-order non-relativistic corrections lead to large contributions, which are not included in the state-of-the-art theoretical predictions. A factorization formula is derived to resum such corrections to all orders in the strong-coupling, and necessary ingredients are calculated to perform the resummation at next-to-leading power. We combine the resummation with fixed-order results and present phenomenologically relevant numerical results. The resummation effect significantly increases the differential cross-section in the threshold region and makes the theoretical prediction more compatible with experimental data. We estimate that using our prediction in the determination of mt
will lead to a value closer to the direct measurement result.
Heavy Higgs bosons at the LHC upgrade *
Authors: Li Tong 
Published: August 2020

Abstract
We evaluate the discovery potential for the heavy Higgs bosons at the LHC energy upgrade with

TeV. We assume the degenerate mass spectrum and an approximate alignment limit in the Type-II Two Higgs Doublet Model for illustration. We explore the observability of the heavy neutral Higgs bosons by examining the clean signals from

via gluon-gluon fusion production. The associated production of a top quark and a charged Higgs boson via

is adopted to predict the discovery potential of heavy charged Higgses. We also emphasize the potential importance of the electroweak production of Higgs boson pairs, i.e.

and

. These are only governed by pure electroweak gauge couplings and can provide complementary information to the conventional signals in the determination of the nature of the Higgs sector.
Systematic study of the α decay preformation factors of the nuclei around the Z = 82, N = 126 shell closures within the generalized liquid drop model *
Authors: Liu Hong-Ming , Zou You-Tian , Pan Xiao , Bao Xiao-Jun , Li Xiao-Hua 
Published: August 2020

Abstract
In this study, we systematically investigate the

decay preformation factors,

, and the

decay half-lives of 152 nuclei around Z = 82, N = 126 closed shells based on the generalized liquid drop model (GLDM) with

being extracted from the ratio of the calculated

decay half-life to the experimental one. The results show that there is a remarkable linear relationship between

and the product of valance protons (holes)

and valance neutrons (holes)

. At the same time, we extract the

decay preformation factor values of the even–even nuclei around the Z = 82, N = 126 closed shells from the study of Sun

[J. Phys. G: Nucl. Part. Phys., 45: 075106 (2018)], in which the

decay was calculated by two different microscopic formulas. We find that the

decay preformation factors are also related to

. Combining with our previous studies [Sun

, Phys. Rev. C, 94: 024338 (2016); Deng

, ibid. 96: 024318 (2017); Deng

, ibid. 97: 044322 (2018)] and that of Seif

[Phys. Rev. C, 84: 064608 (2011)], we suspect that this phenomenon of linear relationship for the nuclei around the above closed shells is model-independent. This may be caused by the effect of the valence protons (holes) and valence neutrons (holes) around the shell closures. Finally, using the formula obtained by fitting the

decay preformation factor data calculated by the GLDM, we calculate the

decay half-lives of these nuclei. The calculated results agree with the experimental data well.
Abnormal odd-even staggering behavior around 132Sn studied by density functional theory *
Authors: Shi Haoqiang , Wang Xiao-Bao , Dong Guo-Xiang , Wang Hualei 
Published: August 2020

Abstract
In this work, we have performed Skyrme density functional theory (DFT) calculations of nuclei around 132Sn to study whether the abnormal odd-even staggering (OES) behavior of binding energies around N = 82 can be reproduced. With the Skyrme forces SLy4 and SkM*, we tested the volume- and surface-type pairing forces and also the intermediate between these two pairing forces, in the Hartree-Fock-Bogoliubov (HFB) approximation with or without the Lipkin-Nogami (LN) approximation or particle number projection after the convergence of HFBLN (PLN). The Universal Nuclear Energy Density Function (UNEDF) parameter sets are also used. The trend of the neutron OES against the neutron number or proton number does not change significantly by tuning the density dependence of the pairing force. Moreover, for the pairing force that is favored more at the nuclear surface, a larger mass OES is obtained, and vice versa. It appears that the combination of volume and surface pairing can give better agreement with the data. In the studies of the OES, a larger ratio of surface to volume pairing might be favored. Additionally, in most cases, the OES given by the HFBLN approximation agrees more closely with the experimental data. We found that both the Skyrme and pairing forces can influence the OES behavior. The mass OES calculated by the UNEDF DFT is explicitly smaller than the experimental one. The UNEDF1 and UNEDF2 forces can reproduce the experimental trend of the abnormal OES around 132Sn. The neutron OES of the tin isotopes given by the SkM* force agrees more closely with the experimental one than that given by the SLy4 force in most cases. Both SLy4 and SkM* DFT have difficulties in reproducing the abnormal OES around 132Sn. Using the PLN method, the systematics of OES are improved for several combinations of Skyrme and pairing forces.