bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-Term Outcomes of Endoscopic Third Ventricle Colloid Cyst Resection: Case Series With a Proposed Grading System
Authors: Isaacs Albert M , Bezchlibnyk Yarema B , Dronyk Jarred , Urbaneja Geberth , Yong Heather , Hamilton Mark G 
Published: January 2020

Abstract

BACKGROUND
Endoscopic resection of colloid cysts has gained recent widespread practice. However, reported complication and recurrence rates are variable, possibly, in part, because of a lack of consistency with reporting of the extent of cyst capsule removal.

OBJECTIVE
To present the long-term outcomes of endoscopic resection of third ventricle colloid cysts without complete capsule removal and propose a grading system to allow consistent description of surgical outcomes.

METHODS
A retrospective review of 74 patients who underwent endoscopic resection of symptomatic third ventricle colloid cysts between 1995 and 2018 was performed. Kaplan-Meier analyses were used to assess recurrence-free survival rates.

RESULTS
Median patient age and cyst diameter were 48.0 (13.0-80.0) yr and 12.0 (5.0-27.0) mm, respectively. Complete emptying of cyst contents with capsule coagulation was achieved in 73 (98.6%) patients. All patients improved or remained stable postoperatively, with a median follow-up duration of 10.3 (0.3-23.7) yr. Radiographic recurrence occurred in 6 (8.1%) patients after their initial surgery, 5 (6.8%) of whom underwent redo endoscopic resection. No major complications or mortality was encountered at primary or recurrence surgery.

CONCLUSION
Endoscopic resection of third ventricle colloid cysts without emphasizing complete capsule removal is a viable option for successfully treating colloid cysts of the third ventricle. Long-term follow-up demonstrates that it is associated with low risks of complications, morbidity, mortality, and recurrence. The proposed extent of the resection grading scheme will permit comparison between the different surgical approaches and facilitate the establishment of treatment guidelines for colloid cysts.
The Reliability of a Grading System for Digital Subtraction Imaging Quality During Cervical Transforaminal Epidural Steroid Injection
Authors: Binler Danielle , House L McLean , Mattie Ryan , Saltychev Mikhail , Nagao Masato , Pekmeczi Murat , Metz Lionel , O’Neil Conor , Shah Vinil , McCormick Zachary L 
Published: January 2020

Abstract

Objective
Digital subtraction imaging (DSI) decreases the risk of intravascular injection during cervical transforaminal epidural steroid injection (CTFESI); however, sequence acquisition and interpretation are operator-dependent skills. This study tests the reliability of a grading system to determine adequate DSI during CTFESI.

Setting
Academic tertiary medical center.

Methods
A grading scheme for adequate DSI quality during CTFESI was created by the study authors based on patient positioning, mask image, and volume of contrast injected. The inter-rater and intrarater reliability values of this grading scheme were tested using 50 DSI images evaluated by three raters during two distinct sessions separated by four weeks. Based on a power analysis, a sample of 50 scans was sufficient to detect significant correlations. Inter-rater reliability was determined by percent agreement between graders for dichotomized categories of “quality of DSI is adequate for safe C-TFESI” vs “quality of DSI is inadequate for safe C-TFESI.” The percentage of agreement was reported, along with Gwet’s agreement coefficient (AC). The intrarater (pre/post) correlation was assessed using Yule’s Q statistics.

Results
Correlation coefficients were interpreted as follows: 0.00–0.19 “very weak,” 0.20–0.39 “weak,” 0.40–0.59 “moderate,” 0.60–0.79 “strong,” and 0.80–1.00 “very strong.” Inter-rater reliability analyses demonstrated that the patient position category had “very strong” agreement, contrast volume had “strong” agreement, and mask image had “moderate” agreement. The overall inter-rater reliability was “moderate.” All of the raters demonstrated “very strong” intrarater reliability.

Conclusions
The proposed grading system for adequate-quality DSI during CTFESI showed overall “moderate” and “very strong” inter- and intrarater reliability, respectively. This scheme provides an objective measure of DSI quality for CTFESI. Refinement is needed to improve the reliability of this scheme.
Predictors of presenteeism, absenteeism and job loss in patients commencing methotrexate or biologic therapy for rheumatoid arthritis
Authors: Gwinnutt James M , Leggett Sarah , Lunt Mark , Barton Anne , Hyrich Kimme L , Walker-Bone Karen , Verstappen Suzanne M M ,   RAMS and BRAGGSS co-investigators
Published: January 2020

AbstractObjectivesWork is an important health outcome. This study aimed to identify predictors of work loss, absenteeism and presenteeism over 1 year in RA patients commencing treatment with MTX or biologics.MethodsPatients aged 18–65 years in full/part-time employment from two UK prospective cohorts were included: MTX-starters = Rheumatoid Arthritis Medication Study; and biologic-starters = Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate. Presenteeism and absenteeism were assessed using the RA-specific Work Productivity Survey at baseline, and 6 and 12 months. Potential predictors including baseline age, gender, clinical measures (e.g. disability, pain, fatigue), psychological distress, occupation and EULAR response from baseline to 6 months were investigated.ResultsA total of 51/463 MTX-starters and 30/260 biologic-starters left work over 12 months. Higher baseline psychological distress in MTX-starters [odds ratio (OR) 1.1 (95% CI: 1.0, 1.1)] and higher disability in biologic-starters [OR 3.5 (95% CI: 1.4, 8.6)] predicted work loss. Some 16.1% of patients reported sick-leave, which was predicted by disability [OR (95% CI): MTX-starters: 1.5 (0.9, 2.3); biologic-starters: 2.4 (1.1, 5.2)]. Median presenteeism scores were very low (minimal interference) in both cohorts. Higher fatigue for MTX starters [incidence rate ratio 1.2 (95% CI: 1.0, 1.4)] and higher disability in biologic-starters (incidence rate ratio 1.4 (95% CI: 1.1, 1.7)] predicted presenteeism. Good EULAR response was associated with lower absenteeism and presenteeism in both cohorts.ConclusionPatients with RA still face significant limitations regarding their ability to work. Disability and EULAR response were the main predictors of work outcomes, emphasizing the need to control the disease and the importance of function in enabling work participation.
Serum CA72-4 is specifically elevated in gout patients and predicts flares
Authors: Bai Xueshan , Sun Mingshu , He Yuwei , Liu Ruhua , Cui Lingling , Wang Can , Wan Fang , Wang Ming , Li Xinde , Li Hailong , Wu Xinjiang , Li Changgui 
Published: January 2020

Abstract

Objectives
Serum CA72-4 levels are elevated in some gout patients but this has not been comprehensively described. The present study profiled serum CA72-4 expression in gout patients and verified the hypothesis that CA72-4 is a predictor of future flares in a prospective gout cohort.

Methods
To profile CA72-4 expression, a cross-sectional study was conducted in subjects with gouty arthritis, asymptomatic hyperuricaemia, four major arthritis types (OA, RA, SpA, septic arthritis) and healthy controls. A prospective gout cohort study was initiated to test the value of CA72-4 for predicting gout flares. During a 6-month follow-up, gout flares, CA72-4 levels and other gout-related clinical variables were observed at 1, 3 and 6 months.

Results
CA72-4 was highly expressed in patients with gouty arthritis [median (interquartile range) 4.55 (1.56, 32.64) U/ml] compared with hyperuricaemia patients [1.47 (0.87, 3.29) U/ml], healthy subjects [1.59 (0.99, 3.39) U/ml] and other arthritis patients [septic arthritis, 1.38 (0.99, 2.66) U/ml; RA, 1.58 (0.95, 3.37) U/ml; SpA, 1.56 (0.98, 2.85) U/ml; OA, 1.54 (0.94, 3.34) U/ml; P &lt; 0.001, respectively]. Gout patients with frequent flares (twice or more in the last year) had higher CA72-4 levels than patients with fewer flares (fewer than twice in the last year). High CA72-4 level (&gt;6.9 U/ml) was the strongest predictor of gout flares (hazard ratio = 3.889). Prophylactic colchicine was effective, especially for patients with high CA72-4 levels (P = 0.014).

Conclusion
CA72-4 levels were upregulated in gout patients who experienced frequent flares and CA72-4 was a useful biomarker to predict future flares.
Strategies for cellular deconvolution in human brain RNA sequencing data
Authors: Sosina Olukayode A. , Tran Matthew N , Maynard Kristen R , Tao Ran , Taub Margaret A. , Martinowich Keri , Semick Stephen A. , Quach Bryan C. , Weinberger Daniel R. , Hyde Thomas M. , Hancock Dana B. , Kleinman Joel E. , Leek Jeffrey T , Jaffe Andrew E 
Published: January 2020

AbstractStatistical deconvolution strategies have emerged over the past decade to estimate the proportion of various cell populations in homogenate tissue sources like brain using gene expression data. Here we show that several existing deconvolution algorithms which estimate the RNA composition of homogenate tissue, relates to the amount of RNA attributable to each cell type, and not the cellular composition relating to the underlying fraction of cells. Incorporating “cell size” parameters into RNA-based deconvolution algorithms can successfully recover cellular fractions in homogenate brain RNA-seq data. We lastly show that using both cell sizes and cell type-specific gene expression profiles from brain regions other than the target/user-provided bulk tissue RNA-seq dataset consistently results in biased cell fractions. We report several independently constructed cell size estimates as a community resource and extend the MuSiC framework to accommodate these cell size estimates (https://github.com/xuranw/MuSiC/).
MQ: Tool for HR-AM Based Quantitative Analysis for Direct MS Workflow
Authors: Ghanate Avinash , Parmar Dharmesh , Bhattacharya Nivedita , Inamdar Ijaz , Phadke Gayatri , Panchagnula Venkateswarlu 
Published: January 2020

AbstractThere is an increased interest in using high-resolution mass spectrometry (HRMS) in the full scan mode (FS) for simultaneous qualitative and quantitative analysis with accurate mass based extracted ion chromatograms (HRMS-AM) for metabolomic profiling workflows. Herein, the capabilities and features of ‘MQ’, a common platform developed to support quantitative analysis from HRMS data are described. Module for qualitative annotation utilizes peak features that include mass accuracy, peak width, and relative abundance of isotopic distribution that offer reliable metabolic confirmation. Additionally, MQ provides multivariate clustering with Principal Component Analysis and a module for high-throughput database query based on user configurable annotated metabolite lists. MQ is capable of handling system-agnostic data formats from both direct HRMS and LC-HRMS analysis. Data processed using MQ for LC-HRMS-AM quantitation of amino acids benchmarked using a commercial tool is presented that validates the quantitative capabilities of the algorithm developed. Datasets representative of three different HRMS-AM based analysis scenarios have been showcased to demonstrate the utility of MQ.Availability and implementationFreely available on web at,http://www.ldims.com/services/software. MQ is implemented in Java and supported on Linux and Microsoft Windows system having Java runtime environment (JRE) pre-installed.
Genomic characterization of three novelPseudomonasphages within the subfamily ofAutographivirinaeisolated from organic waste
Authors: Jørgensen Jacob B , Djuurhus Amaru M , Carstens Alexander B. , Kot Witold , Morris Cindy E. , Hansen Lars H. 
Published: January 2020

AbstractThree phages targetingPseudomonas syringaeGAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to theAutographivirinaesubfamily of the familyPodoviridae.The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera withinAutographivirinae, suggesting that the newly isolated phages could represent a new genus.
A morphological trait involved in reproductive isolation between Drosophila sister species is sensitive to temperature
Authors: Peluffo Alex E. , Hamdani Mehdi , Vargas-Valderrama Alejandra , David Jean R. , Mallard François , Graner François , Courtier-Orgogozo Virginie 
Published: January 2020

AbstractMale genitalia are usually extremely divergent between closely related species, but relatively constant within one species. Here we examine the effect of temperature on the shape of the ventral branches, a male genital structure involved in reproductive isolation, in the sister speciesDrosophila santomeaandD. yakuba. We designed a semi-automatic measurement pipeline that can reliably identify curvatures and landmarks based on manually digitized contours of the ventral branches. With this method, we observed that temperature does not affect ventral branches inD. yakubabut that inD. santomeaventral branches tend to morph into a D. yakuba-like shape at lower temperature. Our results suggest that speciation ofD. santomeaandD. yakubawas associated with a change in genitalia plasticity.
CryoEM structure of the Nipah virus nucleocapsid assembly
Authors: Ker De-Sheng , Jenkins Huw T. , Greive Sandra J. , Antson Alfred A. 
Published: January 2020

AbstractNipah virus is a highly pathogenic zoonotic RNA virus, causing fatal encephalitis in humans. Like other negative-strand RNA viruses including Ebola and measles, its genome is wrapped by the nucleocapsid (N) protein forming a helical assembly. Here we report the CryoEM structure of the Nipah nucleocapsid protein-RNA assembly, at near atomic resolution. The N protein wraps the RNA genome with a periodicity of six nucleotides per protomer, around the outer edge of the helical assembly, in common with other paramyxoviruses. This structure uncovers details of the nucleocapsid assembly, demonstrating the role of the N-terminal arm of the N protein in the formation of the helical assembly and revealing details of the sequence-independent coordination of RNA binding in the “3-bases-in, 3-bases-out” conformation. CryoEM analysis also reveals formation of clam-shaped assemblies of the N-protein, mediated by intersubunit interactions involving several N protein loop regions.
Exploiting evolutionary trade-offs to combat antibiotic resistance
Authors: Melnikov Sergey , Stephens David L. , Fu Xian , Kwok Hui Si , Zhang Jin-Tao , Shen Yue , Sabina Jeffery , Lee Kevin , Lee Harry , Söll Dieter 
Published: January 2020

ABSTRACTAntibiotic resistance frequently evolves through fitness trade-offs in which the genetic alterations that confer resistance to a drug can also cause growth defects in resistant cells. Here, through experimental evolution in a microfluidics-based turbidostat, we demonstrate that antibiotic-resistant cells can be efficiently inhibited by amplifying the fitness costs associated with drug-resistance evolution. Using tavaborole-resistantE. colias a model, we show that genetic mutations in leucyl-tRNA synthetase (that underlie tavaborole resistance) make resistant cells intolerant to norvaline, a chemical analog of leucine that is mistakenly used by tavaborole-resistant cells for protein synthesis. We then show that tavaborole-sensitive cells quickly outcompete tavaborole-resistant cells in the presence of norvaline due to the amplified cost of the molecular defect of tavaborole resistance. This finding illustrates a potentially generalizable approach for combating therapeutic resistance, prolonging the effectiveness of drugs and enabling the use of drugs that are no longer effective due to the rapid evolution of resistance.
Neurons from human mesenchymal stem cells display both spontaneous and stimuli responsive activity
Authors: Karakaş Nihal , Bay Sadık , Türkel Nezaket , Öncül Merve , Bilgen Hülya , Shah Khalid , Şahin Fikrettin , Öztürk Gürkan 
Published: January 2020

ABSTRACTMesenchymal stem cells are one of the promising tissue specific stem cell source for neural tissue regeneration applications. Previous studies on human mesenchymal stem cell (hMSC) derived neurons have been limited and not statisfactory in terms of neuronal activity. In this study, we analysed the functionality of bone marrow hMSCs differentiated into neural protein expressing cells by a single step cytokine based induction protocol. Neurons from both primary hMSCs and hMSC cell line displayed spontaneous activity (≥75%) as demonstrated by Ca++imaging. Furthermore, when electrically stimulated, hMSC induced neurons (hMd-Neuron) matched the response of a typical neuron in the process of maturation. Our results reveal that enriched neurothrophic factors enhance differentiation capacity of bone marrow hMSCs into high yielding functional neurons with spontaneous activity and mature into electrophysiologically active state. hMd-Neurons have the potential to be used as a tool for disease modelling of neuropathologies and neural differentiation studies.
Unrelated males in colonies of facultatively social bee
Authors: Mikát Michael , Benda Daniel , Straka Jakub 
Published: January 2020

AbstractColonies of social Hymenoptera are usually groups of closely related females, in which the dominant female(s) is specialized for reproduction and subordinate females care for immature offspring. Kin selection is thought to be the main factor that supports social cohesion. We have discovered a simple society of the beeCeratina chalybeawith an average of 4.68 colony members that cannot be maintained by kin selection alone. These colonies consisted of old reproductive female, young adults and provisioned brood cells. About half of young adults are unrelated to the old female, and almost all of the young adults are male. The old female provisions new brood cells, while continuing to feed young adult offspring. As young adults do not perform demanding or risky activities, they incur little or no cost, but they do benefit from the food they obtain from the old female.
RADX Sustains POT1 Function at Telomeres to Counteract RAD51 Binding, which Triggers Telomere Fragility
Authors: Briod Anna-Sophia , Glousker Galina , Lingner Joachim 
Published: January 2020

SummaryThe 3’ terminal DNA extensions at chromosome ends can become engaged into multiple biochemical reactions during DNA replication, telomerase-mediated telomere extension, homology directed DNA repair, nucleolytic processing and DNA damage checkpoint activation. To keep these activities in check, telomeric 3’ overhangs can be hidden in t-loop structures or they associate with specialized proteins such as POT1. Here, we explore the telomeric microenvironment using a proximity-dependent labeling approach and identify the oligonucleotide/oligosaccharide-binding (OB)-fold containing protein RADX. RADX binds single-stranded telomeric DNA throughout the cell cycle along with POT1, suppressing accumulation of fragile telomeres, which are indicative of telomere replication defects. Telomere fragility in POT1 and RADX double-depleted cells was due to accumulation of the RAD51 recombinase at telomeres. RADX also supports DNA damage signaling at POT1-depleted telomeres counteracting RAD51 binding. Thus, RADX represents next to POT1 a second OB-fold containing single-strand telomere binding protein sustaining telomere protection.
Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism
Authors: Bezerra Gustavo A. , Foster William R. , Bailey Henry J. , Hicks Kevin G. , Sauer Sven W. , Dimitrov Bianca , Okun Jürgen G. , Rutter Jared , Kölker Stefan , Yue Wyatt W. 
Published: January 2020

ABSTRACTDHTKD1 is a lesser-studied E1 enzyme belonging to the family of 2-oxoacid dehydrogenases. DHTKD1, in complex with the E2 (dihydrolipoamide succinyltransferase, DLST) and E3 (lipoamide dehydrogenase, DLD) components, is implicated in lysine and tryptophan catabolism by catalysing the oxidative decarboxylation of 2-oxoadipate (2OA) in the mitochondria. Here, we solved the crystal structure of human DHTKD1 at 1.9 Å resolution in binary complex with the thiamine diphosphate (ThDP) cofactor. Our structure explains the evolutionary divergence of DHTKD1 from the well-characterized homologue 2-oxoglutarate (2OG) dehydrogenase, in its preference for the larger 2OA substrate than 2OG. InheritedDHTKD1missense mutations cause the lysine metabolic condition 2-aminoadipic and 2-oxoadipic aciduria. Reconstruction of the missense variant proteins reveal their underlying molecular defects, which include protein destabilisation, disruption of protein-protein interactions, and alterations in the protein surface. We further generated a 5.0 Å reconstruction of the human DLST inner core by single-particle electron microscopy, revealing a 24-mer cubic architecture that serves as a scaffold for assembly of DHTKD1 and DLD. This structural study provides a starting point to develop small molecule DHTKD1 inhibitors for probing mitochondrial energy metabolism.
Effect of flagellar beating pattern on sperm rheotaxis and boundary-dependent navigation
Authors: Zaferani Meisam , Javi Farhad , Mokhtare Amir , Abbaspourrad Alireza 
Published: January 2020

AbstractThe study of navigational mechanisms used by mammalian sperm inside a microenvironment yields better understanding of sperm locomotion during the insemination process, which aids in the design of tools for overcoming infertility. Near- and far-field hydrodynamic interactions with nearby boundaries and rheotaxis are known to be some of the steering strategies that keep sperm on the correct path toward the egg. However, it is not known how the beating patterns of sperm may influence these navigational strategies. In this study, we investigate the effect of flagellar beating pattern on navigation of sperm cells both theoretically and experimentally using a two-step approach. We first isolate bovine sperm based on their rheotactic behavior in a zone with quiescent medium using a microfluidic system. This step ensures that the swimmers are able to navigate upstream and have motilities higher than a selected value, even though they feature various flagellar beating patterns. We then explore the flagellar beating pattern of these isolated sperm and their subsequent influence on boundary-dependent navigation. Our findings indicate that rheotaxis enables sperm to navigate upstream even in the presence of circular motion in their motility, whereas boundary-dependent navigation is more sensitive to the circular motion and selects for progressive motility. This finding may explain the clinical importance of progressive motility in semen samples for fertility, as the flow of mucus may not be sufficiently strong to orient the sperm cells throughout the process of insemination.SignificanceFinding the egg and moving toward it while traversing the complex structure of the female reproductive tract is necessary for mammalian sperm. Previous studies have shown how sperm use navigational steering mechanisms that are based on swimming upstream (i.e. rheotaxis) and along the boundaries of the female reproductive tract. We demonstrate that the performance of theses navigational mechanisms is associated with the primary characteristics of sperm motility. In fact, sperm rheotaxis is more sensitive to the motility and thus average velocity of sperm while navigation via rigid boundaries is more sensitive to the flagellar beating pattern and selects for symmetric beating. Our results can be expanded to other autonomous microswimmers and their subsequent navigation mechanisms.