bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meniscal Ramp Lesion Repair Using the FasT-Fix Technique: Evaluating Healing and Patient Outcomes with Second-Look Arthroscopy
Authors: Chen Zhong , Li Wei-Ping , Yang Rui , Song Bin , Jiang Chuan , Hou Jing-Yi , Luo Huan , Zhou Yun-Feng 
Published: September 2017

AbstractAlthough the suture-hook technique remains popular for meniscal ramp lesions, which frequently occur after anterior cruciate ligament (ACL) injury, it is unclear whether the all-inside FasT-Fix technique (Smith & Nephew, Andover, MA) is appropriate for the repair of ramp lesions. This study evaluated results of arthroscopic FasT-Fix meniscal ramp lesion repair using second-look arthroscopy. From August 2010 to December 2014, 46 knees diagnosed with combined ACL injury and ramp lesion underwent ACL reconstruction with meniscal repair using the FasT-Fix technique. We classified ramp lesions into three types according to tear pattern: meniscotibial ligament tear, meniscocapsular tear, and combined meniscotibial/meniscocapsular tear. Second-look arthroscopy was performed postoperatively. The healing capacity of the ramp lesion was evaluated retrospectively. At the final follow-up (mean = 32 months), the Lysholm knee score and the International Knee Documentation Committee (IKDC) objective score were compared with preoperative scores. All patients (n = 46) underwent a second-look arthroscopy, with 45 (97.8%) exhibiting complete or partial healing after the FasT-Fix technique was used in conjunction with ACL reconstruction. The Lysholm knee score and IKDC objective score were significantly better than preoperative scores at final follow-up. The FasT-Fix technique for meniscal ramp lesion repair—when performed with concomitant ACL reconstruction—exhibits excellent healing results.
Defektdeckung an der Hand mit einer seltenen siamesischen Lappenkombination
Authors: Pasternak Itai , Hug Urs , Rüegg Eva , Fritsche Elmar 
Published: September 2017

ZusammenfassungWir berichten über 2 Fälle mit ausgedehnten Weichteildefekten, gleichzeitig den Handrücken und die Handinnenfläche betreffend. Die Defektdeckung erfolgte jeweils mit einer siamesischen Lappenkombination aus einem freien, mikrovaskulär angeschlossenem, weit nach distal gezogenem Oberarmlappen und einer distal gestielten A. interossea posterior Lappenplastik. Wir diskutieren die möglichen Indikationen, Präparationstechnik sowie Vor- und Nachteile dieser selten verwendeten Lappenkombination.
Assessment of quality indicators among nurse practitioners performing upper endoscopy
Authors: Baumgardner Jeffrey , Sewell Justin , Day Lukejohn 
Published: September 2017

Abstract
Background and study aims Limited international data have shown that non-physicians can safely perform upper endoscopy, but no such study has been performed in the United States. Our aim was to assess the quality of outpatient upper endoscopies performed by nurse practitioners (NPs).
Patients and methods Retrospective chart review of upper endoscopies performed by 3 NPs between 2010 and 2013 was performed. Comparisons among all NPs performing upper endoscopy and assessment of individual NP performance over time with respect to quality indicators were performed.
Results Three NPs performed 333 upper endoscopies (distribution of 166, 44, and 123, respectively). Of the cases, 98.2 %s were successfully completed to the second portion of the duodenum. In most cases, photo-documentation of required anatomical landmarks was performed: GE junction (84.2 %), GE junction in retroflexed view (84.2 %), antrum (82.1 %) and duodenum (80.9 %). Photo-documentation improved with increasing experience. NPs appropriately performed biopsies for specific medical conditions: 10/11 (90.9 %) gastric ulcers were biopsied and 63/66 (95.5) of patients with iron deficiency had duodenal biopsies performed for celiac disease. A physician endoscopist was required during the procedure 22.5 % of the time. Important parameters such as documenting informed consent (100 %) and documenting a discharge plan (99.4 %) in the procedure reports were overwhelming present. There was a single adverse event during the study period.
Conclusion In the first US study of NPs performing upper endoscopy, they were able to perform high-quality and safe upper endoscopies. These findings support incorporation of non-physicians alongside physicians to help meet the growing demand for endoscopic services across the United States.
Naturheilverfahren bei Herzinsuffizienz: Hydro-Thermo-Therapie
Authors: Brenke Rainer 
Published: September 2017

ZusammenfassungDurch Naturheilverfahren kann die Therapie der Herzinsuffizienz in vielen Fällen in optimaler Weise ergänzt werden. Im vorliegenden Beitrag
wird der Schwerpunkt auf die heute oft vernachlässigte Hydrotherapie gelegt, denn neue Erkenntnisse, insbesondere zur Sauna und anderen
Maßnahmen der milden Hyperthermie, scheinen ein immenses, therapeutisch noch viel zu wenig genutztes Potenzial zur flankierenden Behandlung
von Herzinsuffizienz zu haben.
Trainingstherapie bei Herzinsuffizienz – Forschungsstand 2017
Authors: Edel Klaus 
Published: September 2017

ZusammenfassungKörperliches Training ist in den aktuellen Leitlinien ein fester Bestandteil der Therapie bei stabiler chronischer Herzinsuffizienz
(Klasse-IA-Indikation) sowohl bei reduzierter als auch bei erhaltener linksventrikulärer Pumpfunktion. Belastung, Symptomatik und
Lebensqualität können durch körperliches Training signifikant verbessert werden. Epidemiologische Daten und verschiedene Studien zeigen,
dass ein aktiver Lebensstil im Alter vor der Entwicklung einer Herzinsuffizienz schützt und ein regelmäßiges körperliches Training das
Risiko einer Herzinsuffizienz reduziert. Die Wirksamkeit ist sowohl dosis- als auch adhärenzabhängig. Empfohlen wird ein Ausdauertraining in
Form eines moderaten, aeroben Trainings („moderate continuous training", MCT), das idealerweise durch ein Krafttraining ergänzt werden
sollte.
Suzaku observations of the outskirts of the galaxy cluster Abell 3395, including a filament toward Abell 3391
Authors: Sugawara Yuuki , Takizawa Motokazu , Itahana Madoka , Akamatsu Hiroki , Fujita Yutaka , Ohashi Takaya , Ishisaki Yoshitaka 
Published: September 2017

Abstract
The results of Suzaku observations of the outskirts of Abell 3395, including a large-scale structure filament toward Abell 3391, are presented. We measured temperature and abundance distributions from the southern outskirt of A 3395 to the north at the virial radius, where a filament structure has been found in the former X-ray and Sunyaev–Zel’dovich (SZ) effect observations between A 3391 and A 3395. The overall temperature structure is consistent with the universal profile proposed by Okabe, N., et al. 2014, PASJ, 66, 99 for relaxed clusters, except for the filament region. A hint of intracluster medium heating is found between the two clusters, which might be due to their interaction in the early phase of a cluster merger. Although we obtained a relatively low metal abundance of $Z=0.169^{+0.164+0.009+0.018 }_{-0.150-0.004-0.015 }$ solar, where the first, second, and third errors are statistical, cosmic X-ray background systematic, and non-X-ray background systematic, respectively, at the virial radius in the filament, our results are still consistent with previous results for other clusters (Z ∼ 0.3 solar) within errors. Therefore, our results are also consistent with the early enrichment scenario. We estimated Compton y parameters only from X-ray results in the region between A 3391 and A 3395 assuming a simple geometry. They are smaller than the previous SZ results with the Planck satellite. The difference could be attributed to a more elaborate geometry such as a filament inclined to the line-of-sight direction, or underestimation of the X-ray temperature because of the unresolved multi-temperature structures or undetected hot X-ray emission of the shock-heated gas.
Optimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network
Authors: Yamada Kazunori D 
Published: September 2017

ABSTRACTA profile comparison method with position-specific scoring matrix (PSSM) is one of the most accurate alignment methods. Currently, cosine similarity and correlation coefficient are used as scoring functions of dynamic programming to calculate similarity between PSSMs. However, it is unclear that these functions are optimal for profile alignment methods. At least, by definition, these functions cannot capture non-linear relationships between profiles. Therefore, in this study, we attempted to discover a novel scoring function, which was more suitable for the profile comparison method than the existing ones. Firstly we implemented a new derivative free neural network by combining the conventional neural network with evolutionary strategy optimization method. Next, using the framework, the scoring function was optimized for aligning remote sequence pairs. Nepal, the pairwise profile aligner with the novel scoring function significantly improved both alignment sensitivity and precision, compared to aligners with the existing functions. Nepal improved alignment quality because of adaptation to remote sequence alignment and increasing the expressive power of similarity score. The novel scoring function can be realized using a simple matrix operation and easily incorporated into other aligners. With our scoring function, the performance of homology detection and/or multiple sequence alignment for remote homologous sequences would be further improved.
Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data
Authors: Rashid Sabrina , Shah Sohrab , Bar-Joseph Ziv , Pandya Ravi 
Published: September 2017

AbstractMotivationIntra-tumor heterogeneity is one of the key confounding factors in deciphering tumor evolution. Malignant cells exhibit variations in their gene expression, copy numbers, and mutation even when originating from a single progenitor cell. Single cell sequencing of tumor cells has recently emerged as a viable option for unmasking the underlying tumor heterogeneity. However, extracting features from single cell genomic data in order to infer their evolutionary trajectory remains computationally challenging due to the extremely noisy and sparse nature of the data.ResultsHere we describe ‘Dhaka’, a variational autoencoder method which transforms single cell genomic data to a reduced dimension feature space that is more efficient in differentiating between (hidden) tumor subpopulations. Our method is general and can be applied to several different types of genomic data including copy number variation from scDNA-Seq and gene expression from scRNA-Seq experiments. We tested the method on synthetic and 6 single cell cancer datasets where the number of cells ranges from 250 to 6000 for each sample. Analysis of the resulting feature space revealed subpopulations of cells and their marker genes. The features are also able to infer the lineage and/or differentiation trajectory between cells greatly improving upon prior methods suggested for feature extraction and dimensionality reduction of such data.Availability and ImplementationAll the datasets used in the paper are publicly available and developed software package is available on Githubhttps://github.com/MicrosoftGenomics/Dhaka.Supporting info and Software:https://github.com/MicrosoftGenomics/Dhaka
Sporosarcina pasteuriican form nanoscale crystals on cell surface
Authors: Bhaduri Swayamdipta , Ghosh Tanushree , Montemagno Carlo , Kumar Aloke 
Published: September 2017

AbstractUsing a semi-solid 0.5% agar column, we study the phenomenon of microbially induced mineral (calcium carbonate) by the bacteriaSporosarcina pasteurii. Our platform allows forin-situvisualization of the phenomena, and we found clear evidence of bacterial cell surface facilitating formation of nanoscale crystals. Moreover, in the bulk agar we found the presence of microspheres, which seem to arise from an aggregation of nanoscale crystals with needle like morphology. Extensive chemical characterization confirmed that the crystals to be calcium carbonate, and two different polymorphs (calcite and vaterite) were identified.
Dissemination ofCryptococcus neoformansvia localised proliferation and blockage of blood vessels
Authors: Gibson Josie F , Evans Robert J , Bojarczuk Aleksandra , Hotham Richard , Lagendijk Anne K , Hogan Benjamin M , Ingham Philip W , Renshaw Stephen A , Johnston Simon A 
Published: September 2017

AbstractCryptococcus neoformansis an opportunistic fungal pathogen that can cause life-threatening cryptoccocal meningitis, predominantly within immunocompromised individuals. Cortical infarcts are observed in as many as 30% of cryptococcal meningitis cases, being particularly common in severe infection. Limited clinical case studies suggest infarcts are secondary to vasculitis and blood vessel damage caused by cryptococcal infection. However, the cause of infarcts in cryptococcal infection has not been determined. To examine potential causes of vascular damage and cryptococcal dissemination in cryptococcal infection, the zebrafishC. neoformansinfection model was used. We demonstrate that spread of cryptococci from the vasculature occurs at sites where cryptococci grow within the blood vessels, originating from a single or small number of cryptococci. We find that cryptococcal cells become trapped within the vasculature and can proliferate there resulting in vasodilation. Localised cryptococcal growth in the vasculature is also associated with sites of dissemination – in some cases simultaneously with a loss of blood vessel integrity. Using a cell-cell junction protein reporter (VE-cadherin) we identified sites dissemination associated with both intact blood vessels and where vessel rupture occurred. Thus, we have identified a mechanism for blood vessel damage during cryptococcal infection that may represent a cause of the vascular damage and cortical infarction observed in cryptococcal meningitis.Author summaryHuman infection by the fungal pathogen,Cryptococcus neoformans, can lead to life-threatening cryptococcal meningitis. In severe cases of cryptococcal meningitis, a lack of blood supply can cause tissue death and a resulting area of dead tissue (infarct) in the brain. Although vasculature inflammation in known to occur in cryptococcal meningitis, the cause of infarcts in unknown. Using a zebrafish model of cryptococcal infection, the growth and dissemination of fungal cells was observed over time. We show that cryptococcal cells become trapped and proliferate in the vasculature, resulting in cryptococcoma that damage the blood vessels. We propose that vessel damage results from increased blood pressure caused by cryptococci blocking blood vessels suggesting that the vascular damage that ensues on cryptococcoma formation may in turn be a cause of infarct formation seen in cryptococcal meningitis.
Specialized plant biochemistry drives gene clustering in fungi
Authors: Gluck-Thaler Emile , Slot Jason C. 
Published: September 2017

AbstractThe fitness and evolution of both prokaryotes and eukaryotes are affected by the organization of their genomes. In particular, the physical clustering of functionally related genes can facilitate coordinated gene expression and can prevent the breakup of co-adapted alleles in recombining populations. While clustering may thus result from selection for phenotype optimization and persistence, the extent to which eukaryotic gene organization in particular is driven by specific environmental selection pressures has rarely been systematically explored. Here, we investigated the genetic architecture of fungal genes involved in the degradation of phenylpropanoids, a class of plant-produced secondary metabolites that mediate many ecological interactions between plants and fungi. Using a novel gene cluster detection method, we identified over one thousand gene clusters, as well as many conserved combinations of clusters, in a phylogenetically and ecologically diverse set of fungal genomes. We demonstrate that congruence in gene organization over small spatial scales in fungal genomes is often associated with similarities in ecological lifestyle. Additionally, we find that while clusters are often structured as independent modules with little overlap in content, certain gene families merge multiple modules in a common network, suggesting they are important components of phenylpropanoid degradation strategies. Together, our results suggest that phenylpropanoids have repeatedly selected for gene clustering in fungi, and highlight the interplay between gene organization and ecological evolution in this ancient eukaryotic lineage.
Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation
Authors: Joo Yoo Jin , Ficarro Scott B. , Soares Luis M. , Chun Yujin , Marto Jarrod A. , Buratowski Stephen 
Published: September 2017

AbstractTFIID binds promoter DNA to recruit RNA polymerase II and other basal factors for transcription. Although the TATA-Binding Protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcription, the TBP-Associated Factor (TAF) subunits recognize downstream promoter elements, act as co-activators, and interact with nucleosomes. Here we show that transcription induces stable TAF binding to downstream promoter DNA, independent of upstream contacts, TBP, or other basal transcription factors. This transcription-dependent TAF complex promotes subsequent activator-independent transcription, and promoter response to TAF mutations in vivo correlates with the level of downstream, rather than overall, Taf1 crosslinking. We propose a new model in which TAFs function as reinitiation factors, accounting for the differential responses of promoters to various transcription factor mutations.
Systemic evidence of acute seizure-associated neuronal injury in patients with temporal lobe epilepsy
Authors: Kunda Shailaja , LaFrance-Corey Reghann G , Khadjevand Fatemeh , Worrell Gregory A , Howe Charles L 
Published: September 2017

AbstractPatients with drug refractory temporal lobe epilepsy frequently accumulate cognitive impairment over time, suggesting neuronal loss induced by seizures. We measured serum levels of neuron-specific enolase (NSE), a neuronal injury marker, relative to levels of S100β, a marker of glial injury, at 6 AM, 9 AM, noon, 3 PM, and 6 PM over the course of several days in 7 epilepsy patients and 4 healthy controls. All epilepsy patients exhibited significant deviations in NSE levels through time, and 4 of the epilepsy patients exhibited large sample entropy values and large signal variation metrics for NSE relative to S100β. Controls did not exhibit such changes. Correlation analysis revealed that NSE levels were significantly elevated after clinical seizure events. There was also a highly significant relationship between increased EEG spike frequency and an increase in serum NSE levels measured 24 hours later. The detection of large but transient post-ictal increases in NSE suggests that even self-limited seizures may cause an injury to neurons that underlies cognitive decline in some patients. Post-ictal assessment of serum NSE may serve as a biomarker for measuring the efficacy of future acute neuroprotective strategies in epilepsy patients.
Floral herbivory does not reduce pollination-mediated fitness in shelter rewarding Royal Irises
Authors: Ghara Mahua , Ewerhardy Christina , Yardeni Gil , Matzliach Mor , Sapir Yuval 
Published: September 2017

ABSTRACTFlorivory, the damage to flowers by herbivores can affect fitness both directly and indirectly. Flowers consumed by florivores may fail to produce fruit or produce lower seed set because of direct damage to reproductive organs. In addition, eaten flowers are less attractive to pollinators because of reduced or modified advertisement, which reduces pollination services. While observational data are abundant, experimental evidence is scarce and results are contrasting. We tested experimentally the effect of florivory on both pollinator visitation and reproductive success in three species of the Royal Irises, which have large flowers that are attractive to pollinators, and potentially also for florivores. We hypothesized that florivory will reduce pollen deposition due to reduced attractiveness to pollinators, while fruit set and seed set will depend on the extent of florivory. We performed artificial florivory in two experiments over two years. In the first experiment, each of the three floral units of a singleIrisflower was subject to either low or high artificial florivory, or left un-touched as control. We counted the number of pollen grains deposited on each of the three stigmas as a measure of pollinator visitation. In the second experiment, three flowers of the same plant received low, high, or no artificial florivory and were further recorded for fruit and seed production. In 2016, high artificial florivory revealed lower number of pollen grains on stigmas ofIris atropurpurea, but in 2017 there was no difference. Similarly, number of pollen grains in high artificial was lower than low florivory in 2017 inI. petrana. No significant effect of florivory was found on pollen grain deposition, fruit set or seed set. The results remained consistent across species and across years. The results undermine the assumption that flower herbivory is necessarily antagonistic interaction and suggests that florivores may not be strong selection agents on floral reproductive biology in theOncocyclusirises.
G-quadruplex secondary structure from circular dichroism spectroscopy
Authors: del Villar-Guerra Rafael , Trent John O. , Chaires Jonathan B. 
Published: September 2017

AbstractA curated library of circular dichroism spectra of 23 G-quadruplexes of known structure was built and analyzed. The goal of this study was to use this reference library to develop an algorithm to derive quantitative estimates of the secondary structure content of quadruplexes from their experimental CD spectra. Principle component analysis and singular value decomposition were used to characterize the reference spectral library. CD spectra were successfully fit to obtain estimates of the amounts of base steps inanti-anti, syn-antioranti-synconformations, in diagonal or lateral loops or in other conformations. The results show that CD spectra of nucleic acids can be analyzed to obtain quantitative structural information about secondary structure content in an analogous way to methods used to analyze protein CD spectra.
A “molecular guillotine” reveals an interphase function of Kinesin-5
Authors: Lv Zhiyi , Rosenbaum Jan , Aspelmeier Timo , Großhans Jörg 
Published: September 2017

AbstractMotor proteins are important for transport and force generation in a variety of cellular processes and morphogenesis. Here we design a general strategy for conditional motor mutants by inserting a protease cleavage site at the “neck” between the head domain and the stalk of the motor protein, making the protein susceptible to proteolytic cleavage at the neck by the corresponding protease. To demonstrate the feasibility of this approach, we inserted the cleavage site of TEV protease into the neck of the tetrameric motor Kinesin-5. Application of TEV protease led to a specific depletion and functional loss of Kinesin-5 in Drosophila embryos. By this, we revealed that Kinesin-5 stabilized the microtubule network during interphase in syncytial embryos. The “molecular guillotine” can potentially be applied to many motor proteins due to the conserved structures of kinesin, dynein and myosin with accessible necks.Author summaryWe design a general strategy for conditional motor mutants by inserting a protease cleavage site between head and stalk domain of the motor protein, making it susceptible to specific proteolytic cleavage. We demonstrate the feasibility of the approach with the motor Kinesin-5 and the protease TEV in Drosophila embryos. This approach can potentially be applied to motor proteins kinesin, dynein and myosin due to the conserved structures.