bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma
Authors: Ennishi Daisuke , Jiang Aixiang , Boyle Merrill , Collinge Brett , Grande Bruno M. , Ben-Neriah Susana , Rushton Christopher , Tang Jeffrey , Thomas Nicole , Slack Graham W. , Farinha Pedro , Takata Katsuyoshi , Miyata-Takata Tomoko , Craig Jeffrey , Mottok Anja , Meissner Barbara , Saberi Saeed , Bashashati Ali , Villa Diego , Savage Kerry J. , Sehn Laurie H. , Kridel Robert , Mungall Andrew J. , Marra Marco A. , Shah Sohrab P. , Steidl Christian , Connors Joseph M. , Gascoyne Randy D. , Morin Ryan D. , Scott David W. 
Published: December 2018

Purpose High-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/TH) has a poor outcome after standard chemoimmunotherapy. We sought to understand the biologic underpinnings of HGBL-DH/TH with BCL2 rearrangements (HGBL-DH/TH- BCL2) and diffuse large B-cell lymphoma (DLBCL) morphology through examination of gene expression. Patients and Methods We analyzed RNA sequencing data from 157 de novo germinal center B-cell-like (GCB)-DLBCLs, including 25 with HGBL-DH/TH- BCL2, to define a gene expression signature that distinguishes HGBL-DH/TH- BCL2 from other GCB-DLBCLs. To assess the genetic, molecular, and phenotypic features associated with this signature, we analyzed targeted resequencing, whole-exome sequencing, RNA sequencing, and immunohistochemistry data. Results We developed a 104-gene double-hit signature (DHITsig) that assigned 27% of GCB-DLBCLs to the DHITsig-positive group, with only one half harboring MYC and BCL2 rearrangements (HGBL-DH/TH- BCL2). DHITsig-positive patients had inferior outcomes after rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone immunochemotherapy compared with DHITsig-negative patients (5-year time to progression rate, 57% and 81%, respectively; P < .001), irrespective of HGBL-DH/TH- BCL2 status. The prognostic value of DHITsig was confirmed in an independent validation cohort. DHITsig-positive tumors are biologically characterized by a putative non–light zone germinal center cell of origin and a distinct mutational landscape that comprises genes associated with chromatin modification. A new NanoString assay (DLBCL90) recapitulated the prognostic significance and RNA sequencing assignments. Validating the association with HGBL-DH/TH- BCL2, 11 of 25 DHITsig-positive–transformed follicular lymphomas were classified as HGBL-DH/TH- BCL2 compared with zero of 50 in the DHITsig-negative group. Furthermore, the DHITsig was shared with the majority of B-cell lymphomas with high-grade morphology tested. Conclusion We have defined a clinically and biologically distinct subgroup of tumors within GCB-DLBCL characterized by a gene expression signature of HGBL-DH/TH- BCL2. This knowledge has been translated into an assay applicable to routinely available biopsy samples, which enables exploration of its utility to guide patient management.
Patient Characteristics, Early Outcomes, and Implementation Lessons of Cervical Cancer Treatment Services in Rural Rwanda
Authors: Park Paul H. , Davey Sonya , Fehr Alexandra E. , Butonzi John , Shyirambere Cyprien , Hategekimana Vedaste , Bigirimana Jean Bosco , Borg Ryan , Uwizeye Regis , Tapela Neo , Shulman Lawrence N. , Randall Thomas , Mpanumusingo Egide , Mpunga Tharcisse 
Published: December 2018

Purpose Low- and middle-income countries account for 86% of all cervical cancer cases and 88% of cervical cancer mortality globally. Successful management of cervical cancer requires resources that are scarce in sub-Saharan Africa, especially in rural settings. Here, we describe the early clinical outcomes and implementation lessons learned from the Rwanda Ministry of Health’s first national cancer referral center, the Butaro Cancer Center of Excellence (BCCOE). We hypothesize that those patients presenting at earlier stage and receiving treatment will have higher rates of being alive. Methods The implementation of cervical cancer services included developing partnerships, clinical protocols, pathology services, and tools for monitoring and evaluation. We conducted a retrospective study of patients with cervical cancer who presented at BCCOE between July 1, 2012, and June 30, 2015. Data were collected from the electronic medical record system and by manually reviewing medical records. Descriptive, bivariable and multivariable statistical analyses were conducted to describe patient demographics, disease profiles, treatment, and clinical outcomes. Results In all, 373 patients met the study inclusion criteria. The median age was 53 years (interquartile rage, 45 to 60 years), and 98% were residents of Rwanda. Eighty-nine percent of patients had a documented disease stage: 3% were stage I, 48% were stage II, 29% were stage III, and 8% were stage IV at presentation. Fifty percent of patients were planned to be treated with a curative intent, and 54% were referred to chemoradiotherapy in Uganda. Forty percent of patients who received chemoradiotherapy were in remission. Overall, 25% were lost to follow-up. Conclusion BCCOE illustrates the feasibility and challenges of implementing effective cervical cancer treatment services in a rural setting in a low-income country.
A Scientometric Profile of Sant Gadge Baba Amravati University, Amravati During 1996-2017
Authors: Bapte Vishal Dattatray , Gedam Jyoti 
Published: December 2018

<p>The study presents the scientometric profile of Sant Gadge Baba Amravati University (SGBAU), Amravati during 1996-2017. The required research output for the study has been pulled out from SCOPUS database on the basis of affiliation based search. The complete research output is 1130 with 11.67% average citations per paper. The highest H-index (17) was found in the year 2013. 20.08% documents were produced though international collaboration. SGBAU, Amravati has the largest collaboration with Brazil (69) and United States (21). Authorship pattern predicts collaborative trend. Research papers produced with three authors have got the maximum (4444) citations. Journals (839) and Conference papers (174) are the most popular source type preferred by the faculty of SGBAU for research expression. Mahendra Rai (209), S. K. Omnwar (143) and Anand S. Aswar (94) are the most prolific authors. It is noteworthy that Alka P. Yadav has got 3073 citations for her 17 papers. Most of the articles are published in the domain of Physics and Astronomy (356). With regard to institutional collaboration, the faculty members of the SGBAU have confined themselves to the Maharashtra state most of the time. Data visualization is carried out using VOSviewer</p><p> </p>
Sex steroid hormone stability in serum tubes with and without separator gels
Authors: Hepburn Sophie , Wright Michael J.P. , Boyder Conchita , Sahertian Renee C. , Lu Ben , Zhang Rui , White Chris P. , Horvath Andrea R. 
Published: December 2018

AbstractBackground:A pilot study showing a decrease in androstenedione concentration in serum collected into gel-containing serum tubes (STs) triggered an investigation of the effect of serum collection tube on steroid hormone stability.Methods:In the main study, two tube types were examined: BD Vacutainer®SST™IIAdvanceand BD Vacutainer®Serum Tube. Forty-seven serum samples from apparently healthy volunteers were collected and analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for testosterone, androstenedione, 17-hydroxyprogesterone (17-OHP) (n=20); and oestradiol (n=27). Primary specimens were centrifuged once, maintained at room temperature and extracted within 2 h for day zero (d0) results. To assess stability following refrigeration (2–8 °C), aliquots were taken from the primary tube on day one (d1) and day five (d5) and analysed immediately. Differences in measurand concentration between tubes at d0 and following storage (d1 and d5) were evaluated for statistical significance.Results:There was a progressive and statistically significant decrease in androstenedione concentration from d0 to d5 (p<0.001) in the SST™II tubes. In addition, there was a statistically significant reduction in testosterone, 17-OHP and oestradiol concentrations at d5 (p<0.01). Interestingly, oestradiol and testosterone concentrations increased with time in plain STs (p<0.01). The only change likely to have a clinical impact was that of androstenedione in serum gel tubes.Conclusions:To optimise conditions and to reduce pre-analytical error we recommend the use of plain serum collection tubes for androstenedione and rapid separation of serum from cells when oestradiol and testosterone are requested.
A full-term infant with type II thanatophoric dysplasia
Authors: Yolanda Natharina , Yulianto Ferry , Arina Sally , Edwin Johanes 
Published: December 2018

Abstract

Objectives
To report a neonate with clinical findings consistent with thanatophoric dysplasia (TD). Only a few cases of this rare and lethal skeletal disorder have been reported in South-East Asia.

Case presentation
A 37-year-old Asian female, fourth gravida at 39 weeks, presented to our hospital for an elective cesarean section due to polyhydramnios, frank breech and gestational hypertension. The father was a 42-year-old Asian male. There was no history of rashes, fever, alcohol intake, substance drug abuse, smoking habit or radiation exposure. Ultrasound (US) of 34-weeks’ gestation found a baby with frontal bossing, prominent temporal lobe, clover-skull and low nasal bridge. The thoracic diameter was smaller than the abdominal diameter. Short limbs without bowing were noted in femur and humeral bones. The patient delivered a baby boy, 4115 g, APGAR scores were 5 and 7 at 1 and 5 min. The baby had a dysmorphic face, frontal bossing, low nasal bridge, low-set ears and short neck. The thorax was narrow and abdomen was protuberant. The upper and lower proximal limbs appeared short. A chest X-ray revealed short, curved ribs and opacification of both lungs. He had respiratory distress shortly after birth and had persistent severe respiratory distress despite adequate mechanical ventilation. On the third day, he had cardiac arrest; resuscitation was not done due to family request. The baby was declared deceased due to cardiopulmonary failure related to his congenital anomaly.

Conclusions
Ultrasonography could readily indicate TD prenatally. The pregnancy can continue up to late third trimester without miscarriage. Most of the neonates die in utero; those who survive are dependent on ventilator.
Mitschwimmen oder untergehen?
Authors: Schoppek Dorothea Elena 
Published: December 2018

AbstractDer Anspruch auf eine tiefgreifende, gesamtgesellschaftliche Transformation stellt die Degrowth-Bewegung vor große Herausforderungen. Abgesehen von weitreichenden strukturellen Veränderungen gilt es, den hegemonialen Wachstums-Diskurs zu durchbrechen und für systemische Alternativen zu mobilisieren. Dieser Beitrag widmet sich der Frage, wie es gelingen kann, einerseits diskursiv anschlussfähig zu bleiben, ohne andererseits vom hegemonialen Diskurs vereinnahmt zu werden. Vor dem Hintergrund verschiedener Strömungen innerhalb des Degrowth-Diskurses, diskutiert Dorothea Schoppek Strategien der Abgrenzung (‚radikaler Bruch‘, ‚Humor‘ und ‚Zukunft als Vergangenheit‘) sowie deren mögliche Konsequenzen auf die Durchsetzungsfähigkeit des Degrowth-Diskurses.
Einstiege in eine demokratische Postwachstums-Transformation
Authors: Adler Frank 
Published: December 2018

AbstractEine PW-Transformation sollte demokratisch, friedlich und maßgeblich durch Druck von unten erfolgen. Realität werden kann diese in der PW-Szene dominante Hoffnung nur, wenn bereits unter den jetzigen Verhältnissen wesentliche Elemente eines PW-kompatiblen Wohlstands für kritische Massen auch der „Durchschnittsbevölkerung“ attraktiv werden. Der Artikel erläutert, welche Inhalte ein PW-kompatibles Modell von Wohlstand haben und auf welche empfundene Defizite im wachstumsorientierten Reproduktionsprozess es damit antworten könnte, inwiefern praktisch erfahrbare Erfolge seiner Verwirklichung zugleich Ursachen für Wachstumsorientierung und Konsumismus suspendieren oder eindämmen können, an welchen Forderungen und Kämpfen politisch relevanter Akteure dabei angeknüpft werden kann und welche Allianzchancen für Degrowth sich damit eröffnen und warum der damit mögliche Druck von unten in radikale strukturelle Reformen münden sollte, die Bedingungen und Akzeptanz für einen wachstumsunabhängigen Wohlstand verbessern, damit auch für weitergehende PW-Transformationen.
Concepts of Phenomenological Irreversible Quantum Thermodynamics I: Closed Undecomposed Schottky Systems in Semi-Classical Description
Authors: Muschik Wolfgang 
Published: December 2018

Abstract
If the von Neumann equation is modified by time dependent statistical weights, the time rate of entropy, the entropy exchange and the production of a Schottky system are derived whose Hamiltonian does not contain the interaction with the system’s environment. This interaction is semi-classically described by the quantum theoretical expressions of power and entropy exchange.
Visual Exegesis at ‘The World’s Oldest Church’: a Case Study for Historiography
Authors: Harrower Scott 
Published: December 2018

Abstract
This article highlights the importance of acknowledging the underlying methodology in the interpretation of early Christian art. I raise these issues via an engagement with the frescoes at Dura Europos, as interpreted by Michael Peppard in his recent work, The World’s Oldest Church. I demonstrate that Peppard’s ideology and archaeological methodology entail a creative, hermeneutical nexus for interpreting the initiation rituals at the Dura Europos house church. For Peppard, this nexus entails an innovative interplay between non-canonical sources, art and liturgical identity. This yields a surprising interpretation of initiation rituals at Dura Europos and, by extension, of early Christianity in Syria. After describing some problematic aspects of Peppard’s ideological and archaeological choices, I offer suggestions for a related proposal on Christology and visual exegesis at the Dura Europos house church baptistery. This proposal begins with clarification of ideological issues that foreground visual exegesis at Dura Europos, and argues for the adoption of six essential criteria when reconstructing the operative Christology in the baptistery of Dura Europos.
Chronic Energy Depletion due to Iron Deficiency Impairs Dendritic Mitochondrial Motility during Hippocampal Neuron Development
Authors: Bastian Thomas W. , von Hohenberg William C. , Georgieff Michael K. , Lanier Lorene M. 
Published: December 2018

During development, neurons require highly integrated metabolic machinery to meet the large energy demands of growth, differentiation, and synaptic activity within their complex cellular architecture. Dendrites/axons require anterograde trafficking of mitochondria for local ATP synthesis to support these processes. Acute energy depletion impairs mitochondrial dynamics, but how chronic energy insufficiency affects mitochondrial trafficking and quality control during neuronal development is unknown. Because iron deficiency impairs mitochondrial respiration/ATP production, we treated mixed-sex embryonic mouse hippocampal neuron cultures with the iron chelator deferoxamine (DFO) to model chronic energetic insufficiency and its effects on mitochondrial dynamics during neuronal development. At 11 days in vitro (DIV), DFO reduced average mitochondrial speed by increasing the pause frequency of individual dendritic mitochondria. Time spent in anterograde motion was reduced; retrograde motion was spared. The average size of moving mitochondria was reduced, and the expression of fusion and fission genes was altered, indicating impaired mitochondrial quality control. Mitochondrial density was not altered, suggesting that respiratory capacity and not location is the key factor for mitochondrial regulation of early dendritic growth/branching. At 18 DIV, the overall density of mitochondria within terminal dendritic branches was reduced in DFO-treated neurons, which may contribute to the long-term deficits in connectivity and synaptic function following early-life iron deficiency. The study provides new insights into the cross-regulation between energy production and dendritic mitochondrial dynamics during neuronal development and may be particularly relevant to neuropsychiatric and neurodegenerative diseases, many of which are characterized by impaired brain iron homeostasis, energy metabolism and mitochondrial trafficking.SIGNIFICANCE STATEMENTThis study uses a primary neuronal culture model of iron deficiency to address a gap in understanding of how dendritic mitochondrial dynamics are regulated when energy depletion occurs during a critical period of neuronal maturation. At the beginning of peak dendritic growth/branching, iron deficiency reduces mitochondrial speed through increased pause frequency, decreases mitochondrial size, and alters fusion/fission gene expression. At this stage, mitochondrial density in terminal dendrites is not altered, suggesting that total mitochondrial oxidative capacity and not trafficking is the main mechanism underlying dendritic complexity deficits in iron-deficient neurons. Our findings provide foundational support for future studies exploring the mechanistic role of developmental mitochondrial dysfunction in neurodevelopmental, psychiatric, and neurodegenerative disorders characterized by mitochondrial energy production and trafficking deficits.
AVery Oil Yellow1Modifier of theOil Yellow1-N1989Allele Uncovers a Cryptic Phenotypic Impact ofCis-regulatory Variation in Maize
Authors: Khangura Rajdeep S , Marla Sandeep , Venkata Bala P , Heller Nicholas J , Johal Gurmukh S , Dilkes Brian P 
Published: December 2018

AbstractForward genetics determines the function of genes underlying trait variation by identifying the change in DNA responsible for changes in phenotype. Detecting phenotypically-relevant variation outside protein coding sequences and distinguishing this from neutral variants is not trivial; partly because the mechanisms by which DNA polymorphisms in the intergenic regions affect gene regulation are poorly understood. Here we utilized a dominant genetic reporter to investigate the effect of cis and trans-acting regulatory variation. We performed a forward genetic screen for natural variation that suppressed or enhanced the semi-dominant mutant allele Oy1-N1989, encoding the magnesium chelatase subunit I of maize. This mutant permits rapid phenotyping of leaf color as a reporter for chlorophyll accumulation, and mapping of natural variation in maize affecting chlorophyll metabolism. We identified a single modifier locus segregating between B73 and Mo17 that was linked to the reporter gene itself, which we call very oil yellow1 (vey1). Based on the variation in OY1 transcript abundance and genome-wide association data, vey1 is predicted to consist of multiple cis-acting regulatory sequence polymorphisms encoded at the wild-type oy1 alleles. The vey1 locus appears to be a common polymorphism in the maize germplasm that alters the expression level of a key gene in chlorophyll biosynthesis. These vey1 alleles have no discernable impact on leaf chlorophyll in the absence of the Oy1-N1989 reporter. Thus, the use of a mutant as a reporter for magnesium chelatase activity resulted in the detection of expression-level polymorphisms not readily visible in the laboratory.
Triacylglycerol Metabolism in Drosophila melanogaster
Authors: Heier Christoph , Kühnlein Ronald P 
Published: December 2018

Abstract
Triacylglycerol (TAG) is the most important caloric source with respect to energy homeostasis in animals. In addition to its evolutionarily conserved importance as an energy source, TAG turnover is crucial to the metabolism of structural and signaling lipids. These neutral lipids are also key players in development and disease. Here, we review the metabolism of TAG in the Drosophila model system. Recently, the fruit fly has attracted renewed attention in research due to the unique experimental approaches it affords in studying the tissue-autonomous and interorgan regulation of lipid metabolism in vivo. Following an overview of the systemic control of fly body fat stores, we will cover lipid anabolic, enzymatic, and regulatory processes, which begin with the dietary lipid breakdown and de novo lipogenesis that results in lipid droplet storage. Next, we focus on lipolytic processes, which mobilize storage TAG to make it metabolically accessible as either an energy source or as a building block for biosynthesis of other lipid classes. Since the buildup and breakdown of fat involves various organs, we highlight avenues of lipid transport, which are at the heart of functional integration of organismic lipid metabolism. Finally, we draw attention to some “missing links” in basic neutral lipid metabolism and conclude with a perspective on how fly research can be exploited to study functional metabolic roles of diverse lipids.
Hough Transform Application to Digitize Rectangular Spatial Objects on Aerospace Imagery
Authors: Miroshnichenko Sergey , Titov Vitalii , Dremov Evgenii , Mosin Sergey 
Published: December 2018

The paper describes the method of development for the remote sensing data processing to speed up the digitizing workflow. The method is designed to digitize rectangular objects using their approximate spatial positions and provides an automatic estimation of the orientation and aspect ratio.
The paper contains a formal statement of the problem of digitizing an object with the desired geometric shape using it’s apriori known spatial position on a source image. The method creates polygonal representations of rectangular spatial objects from one or a few reference points set by an operator. It is based on source image’s pixels clustering using spectral bands as a feature space. The following Hough transform incorporates local direction of intensity gradient to estimate object’s orientation and reduce computational complexity together with low-pass filtering within an accumulation process to improve robustness. It is shown that the developed method can be modified to digitize objects of any analytically described shape.
The method is designed to allow easy user interaction without any significant delays and to provide transparent and predictable control of an output object’s polygon size.
To investigate the developed method a test dataset with more than 700 rectangular objects was used. The root-mean-square error of object’s points positioning, mean rotation error in polar coordinates and a Jaccard index were used to measure a precision of the digitized objects. The experiment results demonstrate that digitizing workflow is accelerated by 25–40% using the software implementing the developed method without a significant precision loss.