bluuebunny/crossref_metadata_2025_split huggingface dataset:
Striatal dopamine deficits predict reductions in striatal functional connectivity in major depression: a concurrent 11C-raclopride positron emission tomography and functional magnetic resonance imaging investigation
Authors: Hamilton J. Paul , Sacchet Matthew D. , Hjørnevik Trine , Chin Frederick T. , Shen Bin , Kämpe Robin , Park Jun Hyung , Knutson Brian D. , Williams Leanne M. , Borg Nicholas , Zaharchuk Greg , Camacho M. Catalina , Mackey Sean , Heilig Markus , Drevets Wayne C. , Glover Gary H. , Gambhir Sanjiv S. , Gotlib Ian H. 
Published: November 2018

AbstractMajor depressive disorder (MDD) is characterized by the altered integration of reward histories and reduced responding of the striatum. We have posited that this reduced striatal activation in MDD is due to tonically decreased stimulation of striatal dopamine synapses which results in decremented propagation of information along the cortico-striatal-pallido-thalamic (CSPT) spiral. In the present investigation, we tested predictions of this formulation by conducting concurrent functional magnetic resonance imaging (fMRI) and 11C-raclopride positron emission tomography (PET) in depressed and control (CTL) participants. We scanned 16 depressed and 14 CTL participants with simultaneous fMRI and 11C-raclopride PET. We estimated raclopride binding potential (BPND), voxel-wise, and compared MDD and CTL samples with respect to BPND in the striatum. Using striatal regions that showed significant between-group BPND differences as seeds, we conducted whole-brain functional connectivity analysis using the fMRI data and identified brain regions in each group in which connectivity with striatal seed regions scaled linearly with BPND from these regions. We observed increased BPND in the ventral striatum, bilaterally, and in the right dorsal striatum in the depressed participants. Further, we found that as BPND increased in both the left ventral striatum and right dorsal striatum in MDD, connectivity with the cortical targets of these regions (default-mode network and salience network, respectively) decreased. Deficits in stimulation of striatal dopamine receptors in MDD could account in part for the failure of transfer of information up the CSPT circuit in the pathophysiology of this disorder.
Image-based promoter prediction: a promoter prediction method based on evolutionarily generated patterns
Authors: Wang Sheng , Cheng Xuesong , Li Yajun , Wu Min , Zhao Yuhua 
Published: November 2018

AbstractPrediction of promoter regions is crucial for studying gene function and regulation. The well-accepted position weight matrix method for this purpose relies on predefined motifs, which would hinder application across different species. Here, we introduce image-based promoter prediction (IBPP) as a method that creates an “image” from training promoter sequences using an evolutionary approach and predicts promoters by matching with the “image”. We used Escherichia coli σ70 promoter sequences to test the performance of IBPP and the combination of IBPP and a support vector machine algorithm (IBPP-SVM). The “images” generated with IBPP could effectively distinguish promoter from non-promoter sequences. Compared with IBPP, IBPP-SVM showed a substantial improvement in sensitivity. Furthermore, both methods showed good performance for sequences of up to 2,000 nt in length. The performances of IBPP and IBPP-SVM were largely affected by the threshold and dimension of vectors, respectively. The source code and documentation are freely available at https://github.com/hahatcdg/IBPP.
A minimum information standard for reproducing bench-scale bacterial cell growth and productivity
Authors: Hecht Ariel , Filliben James , Munro Sarah A. , Salit Marc 
Published: November 2018

AbstractReproducing, exchanging, comparing, and building on each other’s work is foundational to technological advances. Advancing biotechnology calls for reliable reuse of engineered organisms. Reliable reuse of engineered organisms requires reproducible growth and productivity. Here, we identify the experimental factors that have the greatest effect on the growth and productivity of our engineered organisms in order to demonstrate reproducibility for biotechnology. We present a draft of a Minimum Information Standard for Engineered Organism Experiments (MIEO) based on this method. We evaluate the effect of 22 factors on Escherichia coli engineered to produce the small molecule lycopene, and 18 factors on E. coli engineered to produce red fluorescent protein. Container geometry and shaking have the greatest effect on product titer and yield. We reproduce our results under two different conditions of reproducibility: conditions of use (different fractional factorial experiments), and time (48 biological replicates performed on 12 different days over 4 months).
Auf dem Sprung
Authors: Bleher Chris 
Published: November 2018

ZusammenfassungPlyo, Cat Leap, Präzi – in der urbanen Trendsportart Parkour trainieren schon
Kinder Bewegungsmuster, die einst französische Vietnam-Krieger für die Flucht im
Dschungel konzipierten. Längst profitieren Unterhaltungsindustrie und
Sportorganisationen vom Boom. Doch wer nur Aufmerksamkeit sucht, statt sich in
Geduld und Achtsamkeit zu üben, landet schneller auf dem OP-Tisch als in der
sicheren Hocke. Besuch bei einem Protagonisten der Szene.
Optimale Belastung während der Rehabilitation nach einer
Patellatendinopathie: eine Fallstudie
Authors: Cook Jill , Docking Sean , Girdwood Michael , Bonello Christian , Hannington Madeline , Rio Ebonie 
Published: November 2018

ZusammenfassungWenn das Knie schmerzt, ist das nicht nur lästig. Es kann auch sehr schnell mit
der Leistung bergab gehen. Um eine lange Verletzungspause zu vermeiden und
schnell wieder auf das altes Niveau zurückzukehren, ist neben einer fundierten
Untersuchung auch eine optimale Therapieplanung wichtig.
Blood Flow Restriction Training nach Rekonstruktion des
vorderen Kreuzbandes
Authors: Pröger Stefan , Kurz Eduard , Brehme Kay , Pyschik Martin , Schwesig René , Bartels Thomas 
Published: November 2018

Zusammenfassung„Mehr Gewicht“; „Training bis zur Erschöpfung“; „immer wieder neue Reize“ –
Schlagworte, die man häufig hört, wenn man danach fragt, wie ein optimales
Training aussehen soll. Doch welche Methode ist nun die beste, um effektiv
Muskulatur und Kraft aufzubauen? Blood Flow Restriction Training eröffnet in
diesem Kontext neue Perspektiven. Es verspricht schnellen Erfolg mit geringerem
Aufwand. Gibt es berechtigte Hoffnung, dass man mit Okklusionstraining nach
Operationen früher wieder fit wird als mit anderen Methoden? Die Antwort ist
nicht ganz einfach.
Adipose-Based Therapies for Knee Pain—Fat or Fiction
Authors: Shimozono Yoshiharu , Fortier Lisa , Brown Donald , Kennedy John 
Published: November 2018

AbstractRegenerative cell therapies are emerging as promising treatments for numerous musculoskeletal conditions, including knee osteoarthritis (OA). Adipose-derived stem cells and possibly other adipose-based therapies have a greater chondrogenic potential than stem cells derived from bone marrow, and thus a lot of attention is being placed on them as potential regenerative agents in the treatment of knee OA. Several types of adipose-based therapies have good basic science and preclinical data supporting their translation to human therapeutic intervention. Cultured, adipose-derived stem cells appear to be good source of bioactive cells with convenient accessibility, relative abundance, and well-documented regenerative capacity. Non-culture expanded adipose-based therapy, in the forms of stromal vascular fraction and most recently micronized adipose tissue (MAT), have been utilized in patients to treat OA and other cartilage abnormalities with encouraging preliminary data. These adipose-based therapies have shown a lot of therapeutic potential; however, because of the regulatory restrictions on enzymatic isolation and cell expansion, only MAT is currently available in clinical practice in the United States. While no serious adverse reactions have been reported, adipose-derived therapies also have the potential for adverse reactions including inflammation and infection. The current review provides an update on the latest research and presents this evidence on the therapeutic potential of adipose-based therapies in the treatment of knee OA.
Endoscopic Pancreato-Biliary Interventions
Authors: Raza Ali , Krishnan Kumar 
Published: November 2018

AbstractEndoscopic ultrasound (EUS) and endoscopic retrograde cholangiopancreatography (ERCP) play a critical role in the diagnosis and management of benign and malignant pancreatobiliary diseases. In the last several years, role of ERCP has evolved from just a diagnostic procedure to mostly a therapeutic procedure. It plays a key role in the diagnosis of indeterminate biliary strictures and evaluation of bile leaks. Therapeutic ERCP utilizes various techniques for the extraction of biliary and pancreatic stones, management of bile leaks, and the treatment of malignant and benign strictures. EUS plays a central role in tissue acquisition for diagnostic purposes. Therapeutic applications of EUS have significantly increased in the recent years and include management of pancreatic fluid collections, pancreatic necrosis, drainage of the biliary obstruction, gall bladder drainage, and EUS-assisted ERCP. These procedures have good efficacy and acceptable side effect profile when performed by expert endoscopists at tertiary care medical centers.
Transcriptional Activity of Human Endogenous Retroviruses in Response to Prenatal Exposure of Maternal Cigarette Smoking
Authors: Bergallo Massimiliano , Galliano Ilaria , Daprà Valentina , Pirra Alice , Montanari Paola , Pavan Marzia , Calvi Cristina , Bertino Enrico , Coscia Alessandra , Tovo Pier-Angelo 
Published: November 2018

Objective Transcription of human endogenous retrovirus (HERV) elements is usually suppressed by epigenetic factors such as DNA methylation and heterochromatin silencing by histone modifications. There is an association between maternal smoking during pregnancy and DNA methylation levels in placental tissue and in DNA from cord blood.
Study Design We assessed the transcriptional activity of HERV-H, HERV-K, and HERV-W in umbilical cord blood from 47 term babies unexposed to tobacco smoke in utero and 23 term babies exposed to tobacco smoke in utero.
Results In our population, the HERV-H, HERV-K, and HERV-W families were always transcriptionally active, and the levels of all HERVs (H, K, W) were significantly higher in unexposed than smoke-exposed babies.
Conclusion This study provides preliminary information about the transcriptional activity of HERV-H, HERV-K, and HERV-W families in human umbilical cord blood.
Relationship between Early Antibiotic Exposure and Short-Term Growth Velocity in Premature Neonates
Authors: Reid Brittany M. , Eisenberg Ruth , Forman Katie , LaTuga Mariam Susan 
Published: November 2018

Objective To characterize the relationship between the duration of antibiotic administration during the first week of life and subsequent growth velocity during hospitalization.
Study Design This was a retrospective study comparing the inhospital growth of infants born between 30 and 326/7 weeks' gestational age (GA) admitted to the Montefiore Weiler and Wakefield neonatal intensive care units between January 2009 and December 2015. Antibiotic duration during the first week of life was classified as no antibiotics, <5 days of antibiotics, or ≥5 days of antibiotics. Differences between discharge and birth weight Z-scores were compared between the three groups using analysis of variance.
Results Of the infants, 87% received antibiotics during the first week of life, with 16% of infants completing ≥5 days. Compared with infants receiving ≤ 5 days of antibiotics, infants treated with ≥5 days had a lower GA, lower Apgar scores, more invasive respiratory support, longer duration of total parenteral nutrition, delayed initiation of enteral feeding, and a higher weight Z-score on admission and discharge (p < 0.05). However, there was no distinction in growth between the three groups assessed by the difference between admission and discharge weight Z-scores (p = 0.64), growth velocity (gram/kilogram/day) (p = 0.104), or an exponential growth velocity outcome (p = 0.423).
Conclusion Early antibiotic exposure was not associated with increased growth velocity between birth and discharge. Our study was limited by its retrospective nature and lack of follow-up data postdischarge.
Tension Pneumocephalus after Cervical Spine Surgery: A Case Report with Review of the Literature
Authors: Maupin Jeremiah , Burrow Zackary , Shirazi Cameron , Vallurupalli Santaram 
Published: November 2018

AbstractThis is the case of a 66-year-old male with cervical myelopathy secondary to severe cervical stenosis manifesting as worsening dexterity and numbness in his right hand. The patient underwent C3–C6 laminoplasty with bilateral foraminotomies. During the procedure an incidental durotomy occurred which was patched intraoperatively with Duragen and Tisseel. At 1 month follow-up, the patient reported that he was doing well and skin sutures were removed. Two days later, the patient presented to the emergency department with postoperative wound dehiscence, cerebrospinal fluid (CSF) drainage, altered mental status and lethargy. At that time, a computed tomography (CT) scan confirmed a tension pneumocephalus which was treated with a cranial burr hole and revision durotomy repair. The patient improved and was discharged to a rehabilitation facility with intact motor and cognitive function. At the 1-year follow-up appointment, he continued to do well without sequelae.
Tinnitus Management in Lateral Skull Base Lesions
Authors: Juan Juan , Basura Gregory 
Published: November 2018

AbstractTinnitus, the phantom perception of sound in the absence of a physical sound source, is a complex problem with multiple etiologies. While most commonly presenting in a subjective fashion caused by measurable hearing loss, other etiologies including lateral skull base tumors that encroach on middle and inner ear structures can lead to phantom sound perception as well. In addition to discussing the basic background of tinnitus, here we also review current theories of etiology that include central auditory and nonauditory neural mechanisms and potential treatments that range from sound therapy to medications to cognitive and behavioral therapies and cranial nerve and brain stimulation. One main purpose of this article is to relate tinnitus causes to skull base tumors, surgical removal, and resultant sequelae, including damage to cranial nerves resulting in audiovestibular dysfunction. We also discuss the utility of microvascular decompression for both tumor and nontumor-associated tinnitus and the current literature regarding hearing preservation rates and tinnitus perception, where documented, with the three common treatment modalities employed for most lateral skull base tumors that includes watchful waiting with serial imaging, stereotactic radiosurgery and primary surgical resection using hearing preservation and hearing ablative approaches. The management of skull base tumors is a complex process that depending upon the approach and sequelae, may lead to manageable or worsening phantom sound perception that must be considered when discussing the multiple treatment options with patients.
Fluorine in the structure of polymers: influence on the gas separation properties
Authors: Yampolskii Yuri P. , Belov Nikolay A. , Alentiev Alexandre Yu. 
Published: November 2018

Results of studies on the separation of gases and vapours using fluorine-containing polymers are integrated and analyzed. Methods for the synthesis of these polymers are considered, including direct gas-phase fluorination, plasma polymerization of fluorine-containing precursors and modification of organic polymers, as well as diverse syntheses of monomers containing C−F and C−CF3 bonds and their subsequent polymerization. Structure – property relationships for these polymers are elucidated and their actual and potential applications as membrane materials are discussed.
The bibliography includes 165 references.
Intrinsic TNFR2 signaling in T regulatory cells provides protection in CNS autoimmunity
Authors: Atretkhany Kamar-Sulu N. , Mufazalov Ilgiz A. , Dunst Josefine , Kuchmiy Anna , Gogoleva Violetta S. , Andruszewski David , Drutskaya Marina S. , Faustman Denise L. , Schwabenland Marius , Prinz Marco , Kruglov Andrey A. , Waisman Ari , Nedospasov Sergei A. 
Published: November 2018

SignificanceIn spite of TNF involvement in the pathogenesis of multiple sclerosis (MS), systemic TNF neutralization in MS patients was not successful. One of the possible reasons is that TNF possesses both pathogenic and protective features that may be related to TNFR1 versus TNFR2 receptor engagement. This study uncovers one of such protective functions of TNF mediated by intrinsic TNFR2 signaling in Tregcells. In mice bearing humanized TNF and TNFR2 genetic loci, TNFR2 ablation restricted to Tregcells led to reduced capacity to control Th17 cell responses, exacerbated experimental autoimmune encephalomyelitis (EAE) development, and affected the maintenance of Tregcells. These findings provide support for the emerging role of TNFR2 signaling in autoimmunity, as demonstrated here in mice with conditional inactivation of TNFR2.
Genetic recovery of ErbB4 in adulthood partially restores brain functions in null mice
Authors: Wang Hongsheng , Liu Fang , Chen Wenbing , Sun Xiangdong , Cui Wanpeng , Dong Zhaoqi , Zhao Kai , Zhang Hongsheng , Li Haiwen , Xing Guanglin , Fei Erkang , Pan Bing-Xing , Li Bao-Ming , Xiong Wen-Cheng , Mei Lin 
Published: November 2018

SignificanceNRG1–ErbB4 signaling is implicated in GABAergic circuit assembly during development and GABAergic transmission at adulthood. However, it is unclear whether phenotypes in the adult stage in ErbB4 mutant mice result from abnormal neural development. By using two strains of mice with temporal control of ErbB4 deletion and expression, we demonstrate that ErbB4 deletion in adult mice impaired behavior and GABA release, whereas deficits due to ErbB4 null mutation during development were alleviated by restoring ErbB4 expression at the adult stage. Together, our results indicate that NRG1–ErbB4 signaling at adulthood is critical to GABAergic transmission and behavior and suggest that restoring NRG1–ErbB4 signaling at the postdevelopmental stage might benefit relevant brain disorders.
Parthenium weed: uses and abuses.
Authors: Nimal Chandrasena Nimal Chandrasena , Rao A. N. 
Published: November 2018

Abstract

There has been a debate about the potential role of utilization in management of parthenium weed (Parthenium hysterophorus). A large volume of published material is available on potential uses of this weed and opportunities for further exploitation. This chapter critically reviews this published information on the actual uses of the plant in different countries. It also weighs the benefits and potential problems associated with utilization of this weed in countries where existing infestations are large and threaten to spread further. It also explores the question: should utilization be considered an effective management tool in countries such as India, to manage existing infestations and prevent its further spread? It is concluded that the risks of spread and the overall negative economic, social and environmental impacts of parthenium weed may far outweigh its potential benefits, particularly in regions susceptible to new invasions. Therefore, a precautionary approach is suggested in promoting utilization of parthenium weed, not least because failure to do so would undermine the current efforts to contain its spread across many countries in Asia, South-east Asia, Africa and Australia.
History and management - Southern Asia.
Authors: Asad Shabbir Asad Shabbir , Shrestha B. B. , Ali M. H. , Adkins S. W. 
Published: November 2018

Abstract

In Southern Asia, parthenium weed (Parthenium hysterophorus) is now present in most countries, including India, Pakistan, Sri Lanka, Nepal, Bangladesh and Bhutan. Although there are no confirmed reports of its presence in Afghanistan or Maldives, it is highly likely that it is present in Afghanistan. This chapter discusses the history of invasion, background, spread and management of pathenium weed in Southern Asia. Parthenium weed, arguably the most important invasive plant species in Southern Asia, is well adapted to thrive in the wide-ranging habitats of this region, making management extremely difficult. One conclusion reached is that only an integrated management approach, which involves a suite of strategies (cultural, physical, biological and chemical), will be effective in managing this weed on a long-term and sustainable basis in this region. Management has to be viewed in the long term and needs to involve collaboration across states, regions and countries, as there seems to be no 'silver bullet' solution to this challenging weed.
Large‐scale, cross‐flow based isolation of highly pure and endocytosis‐competent extracellular vesicles
Authors: McNamara Ryan P. , Caro‐Vegas Carolina P. , Costantini Lindsey M. , Landis Justin T. , Griffith Jack D. , Damania Blossom A. , Dittmer Dirk P. 
Published: November 2018

ABSTRACTIsolation of extracellular vesicles (EVs) from cell culture supernatant or plasma can be accomplished in a variety of ways. Common measures to quantify relative success are: concentration of the EVs, purity from non‐EVs associated protein, size homogeneity and functionality of the final product. Here, we present an industrial‐scale workflow for isolating highly pure and functional EVs using cross‐flow based filtration coupled with high‐molecular weight Capto Core size exclusion. Through this combination, EVs loss is kept to a minimum. It outperforms other isolation procedures based on a number of biochemical and biophysical assays. Moreover, EVs isolated through this method can be further concentrated down or directly immunopurified to obtain discreet populations of EVs. From our results, we propose that cross‐flow/Capto Core isolation is a robust method of purifying highly concentrated, homogenous, and functionally active EVs from industrial‐scale input volumes with few contaminants relative to other methods.
iHam and pyHam: visualizing and processing hierarchical orthologous groups
Authors: Train Clément-Marie , Pignatelli Miguel , Altenhoff Adrian , Dessimoz Christophe 
Published: November 2018

Abstract

Summary
The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species.

Availability and implementation
iHam’s code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam’s code is available at https://github.com/DessimozLab/pyHam and or via the pip package ‘pyham’.