bluuebunny/crossref_metadata_2025_split huggingface dataset:
One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification
Authors: Minot Samuel S. , Krumm Niklas , Greenfield Nicholas B. 
Published: September 2015

1ABSTRACTHigh-throughput sequencing (HTS) is increasingly being used for broad applications of microbial char-acterization, such as microbial ecology, clinical diagnosis, and outbreak epidemiology. However, the analytical task of comparing short sequence reads against the known diversity of microbial life has proved to be computationally challenging. The One Codex data platform was created with the dual goals of analyzing microbial data against the largest possible collection of microbial reference genomes, as well as presenting those results in a format that is consumable by applied end-users. One Codex identifies microbial sequences using a“k-mer based” taxonomic classification algorithm through a web-based data platform, using a reference database that currently includes approximately 40,000 bacterial, viral, fungal, and protozoan genomes. In order to evaluate whether this classification method and associated database provided quantitatively different performance for microbial identification, we created a large and diverse evaluation dataset containing 50 million reads from 10,639 genomes, as well as sequences from six organisms novel species not be included in the reference databases of any of the tested classifiers. Quantitative evaluation of several published microbial detection methods shows that One Codex has the highest degree of sensitivity and specificity (AUC = 0.97, compared to 0.82-0.88 for other methods), both when detecting well-characterized species as well as newly sequenced, “taxonomically novel” organisms.
Tyrosination of α-Tubulin Controls The Initiation of Processive Dynein-Dynactin Motility
Authors: McKenney Richard J. , Huynh Walter , Vale Ronald D. , Sirajuddin Minhaj 
Published: September 2015

ABSTRACTPost-translational modifications (PTMs) of α/β-tubulin are believed to regulate interactions with microtubule binding proteins. A well-characterized PTM involves the removal and re-ligation of the C-terminal tyrosine on α-tubulin, but the purpose of this tyrosination-detyrosination cycle remains elusive. Here, we examined the processive motility of mammalian dynein complexed with dynactin and BicD2 (DDB) on tyrosinated versus detyrosinated microtubules. Motility was decreased ~4-fold on detyrosinated microtubules, constituting the largest effect of a tubulin PTM on motor function observed to date. This preference is mediated by dynactin’s microtubule binding p150 subunit rather than dynein itself. Interestingly, on chimeric microtubules, DDB molecules that initiated movement on tyrosinated tubulin continued moving into a region of detyrosinated tubulin. This result indicates that the α-tubulin tyrosine facilitates initial motor-tubulin encounters, but is not needed for subsequent motility. Our results reveal a strong effect of the C-terminal α-tubulin tyrosine on dynein-dynactin motility and suggest that the tubulin tyrosination cycle could modulate the initiation of dynein-driven motility in cells.
Liverworts to the rescue: an investigation of their efficacy as mycorrhizal inoculum for vascular plants
Authors: Kowal Jill , Pressel Silvia , Duckett Jeffrey G. , Bidartondo Martin I. 
Published: September 2015

Summary

Pezoloma ericae (D.J. Read) Baral, a widespread mycorrhizal fungus of plants in the Ericales, is known to form intracellular associations with several families of leafy liverworts (Schistochilaceae, Lepidoziaceae, Cephaloziaceae, Cephaloziellaceae) in vitro. The ecological significance of this link between vascular and non‐vascular plants is unknown.

Fungal symbionts were isolated from rhizoids of the leafy liverworts Cephalozia connivens (Dicks.) Lindb. and C. bicuspidata (L.) Dum. (Cephaloziaceae), as well as from the hair roots of two dominant ericoid mycorrhiza‐forming species of European heathlands, Erica tetralix (L.) and Calluna vulgaris (L.).

Using pure cultures of P. ericae, we resynthesized liverwort–fungus associations to use colonized liverworts as inoculum which was applied to substrates supporting the growth of heather seedlings and cuttings. Effects were quantified using germination, rooting, plant colonization, plant survival under waterlogging stress and growth in height in experimental systems with and without liverworts and/or fungi.

Fungal symbionts growing from liverwort rhizoids readily colonized the hair roots of ericaceous plants to form typical ericoid mycorrhizas.

The presence of inoculum‐bearing liverworts led to significant increases in plant growth. Erica tetralix was more responsive to inoculation than C. vulgaris.

Ericaceous cuttings rooted and survived more successfully when they were coplanted with previously colonized liverwort stems.

We demonstrate, under realistic ecological circumstances, that liverworts can deliver mycorrhizal inoculum and improve the establishment of vascular plants. We propose that by providing sources of mycorrhizal inoculum, symbiotic non‐vascular plants can contribute to the restoration of plant communities dominated by Ericales plants. This research leads to broader knowledge about the function of ericoid mycorrhizas in ecosystems.
Combination Inhibition Activity of Nisin and Ethanol on the Growth Inhibition of Pathogenic Gram Negative Bacteria and Their Application as Disinfectant Solution
Authors: Phongphakdee Komsan , Nitisinprasert Sunee 
Published: September 2015

AbstractNisin and ethanol have been used as antimicrobial agents in food industry. However, nisin alone could not inhibit the growth of gram‐negative bacteria, except in combination with a chelating agent, EDTA, or organic acid. This research aimed to study the survival of Escherichia coli O157: H7, Salmonella Typhimurium TISTR 292 and Salmonella Enteritidis DMST 17368 after treatment with nisin at 100, 200, 300, 500, 800, or 1000 IU/mL and ethanol at 70%, 50%, 30%, 20%, or 10% (v/v) alone and in combination. None of all nisin concentrations could reduce the growth of target strains. While 20% ethanol (v/v) having no negative effect on human health, could slightly reduce the growth of target strains. However, the combination of nisin at 500, 800 or 1000 IU/mL and 20% ethanol displayed significant growth reduction at 15 min were below 1 log CFU/mL. Thus, the minimum inhibitory concentration of nisin and ethanol was 500 IU/mL and 20% (v/v), respectively. The release of fatty acid, genetic materials and scanning electron microscope suggested that nisin‐ethanol treated cells have altered permeability causing bacterial growth inhibition. Comparison treatment of combined solution and commercial chloride based sanitizer were done for all target strains on stainless steel surface. Survivals of three target strains were below 1 log CFU/mL. The result suggested that combined solution of nisin and ethanol may be a beneficial sanitizer for food industry to inhibit the growth of E. coli O157:H7 and Salmonella sp.
Enzymatic Synthesis of Refined Olive Oil‐Based Structured Lipid Containing Omega ‐3 and ‐6 Fatty Acids for Potential Application in Infant Formula
Authors: Li Ruoyu , Sabir Jamal S. M. , Baeshen Nabih A. , Akoh Casimir C. 
Published: September 2015

AbstractStructured lipids (SLs) containing palmitic, docosahexaenoic (DHA), and gamma‐linolenic (GLA) acids were produced using refined olive oil, tripalmitin, and ethyl esters of DHA single cell oil and GLA ethyl esters. Immobilized Lipozyme TL IM lipase was used as the biocatalyst. The SLs were characterized for fatty acid profile, triacylglycerol (TAG) molecular species, solid fat content, oxidative stability index, and melting and crystallization profiles and compared to physical blend of substrates, extracted fat from commercial infant formula (IFF), and milk fat. 49.28 mol% of palmitic acid was found at the sn‐2 position of SL TAG and total DHA and GLA composition were 0.73 and 5.00 mol%, respectively. The total oleic acid content was 36.13 mol% which was very close to the 30.49% present in commercial IFF. Comparable solid fat content profiles were also found between SLs and IFF. The SLs produced have potential for use in infant formulas.
Classification of semi‐automated flare readings using the Kowa FM 700 laser cell flare meter in patients with uveitis
Authors: Agrawal Rupesh , Keane Pearse A. , Singh Jasmin , Saihan Zubin , Kontos Andreas , Pavesio Carlos E. 
Published: September 2015

AbstractPurposeTo propose a classification system to grade semi‐automated flare readings and assess its correlation with clinical flare grading and also to explore the utility of an additional step in clinical flare assessment between grades 0 and 1.MethodsSemi‐automated flare readings from 103 eyes with uveitis were taken using the Kowa FM 700 laser flare meter and classified into two models (LFCM and LFCM_1), and introduction of a 0.5 step in flare grading was explored.ResultsGood correlation was present between the conventional SUN clinical flare and the proposed clinical classification for flare (weighted kappa (WK) = 89.64%, p < 0.001). Semi‐automated flare grading (LFCM and LFCM_1) had WK agreement of 82.52% and 79.85% (p < 0.001) with conventional SUN clinical flare grading.ConclusionsThe proposed classification system for semi‐automated laser flare readings (LFCM) allows stratification of measurements into grades analogous to clinical flare grades and correlates well with conventional clinical flare grading.
The Danish version of the Radner Reading Chart: design and empirical testing of sentence optotypes in subjects of varying educational background
Authors: Munch Inger Christine , Jørgensen Astrid‐Helene Ravn , Radner Wolfgang 
Published: September 2015

AbstractPurposeTo develop 28 short texts to be used as sentence optotypes in a Danish version of the Radner Reading Chart for the measurement of reading acuity and speed.MethodForty‐six short texts of comparable lexical and grammatical difficulty were constructed. The short texts were tested together with two longer reference texts in 100 persons with visual acuity 6/6, of which 50 were university students (age: 24.7 ± 3.1 years, 36% males) and 50 were blue‐collar workers (37.2 ± 13.4 years, 54% males). Study parameters were mean reading speed and error rate per participant, and mean reading time, variance and number of errors per short text.ResultsThe students read the short texts faster than the blue‐collar workers (184 ± 21.4 words per minute (wpm) versus 163 ± 26.3 wpm, p < 0.0001). There was a high correlation between the reference texts and the short texts [Pearson's correlation coefficient = 0.89 (95% CI 0.83–0.92)]. The mean reading time for each of the short texts ranged from 4.4 s to 5.8 s with a mean of 4.96 ± 0.35 s, and the median number of errors was eight. Twenty‐eight short texts were selected for sentence optotypes with mean reading times between 4.6 s and 5.2 s, a mean standard deviation of 1.2 s or less and a number of errors of 17 per 100 persons or less.ConclusionReading time uniformity in the Danish version of the Radner Reading Chart was comparable to that of the original German version. Education had an influence on reading performance that may warrant stratification for this parameter when reading tests are used in clinical trials.
Extremely elevated C‐reactive protein levels are associated with unfavourable outcomes, including death, in paediatric patients
Authors: Pasternak Yehonatan , Livni Gilat , Ashkenazi Shai , Lowenthal Alexander , Yarden‐Bilavsky Havatzelet 
Published: September 2015

AbstractAimThe aim of this study was to investigate the clinical significance of extremely elevated C‐reactive protein (CRP) levels in hospitalised children.MethodsWe searched the electronic database of a tertiary paediatric medical centre for all patients admitted in 2010–2013 with a CRP of ≥30 mg/dL, and these comprised the study group. The controls were the other admissions. Data were collected on demographics, admission details, pre‐existing conditions, discharge diagnosis, laboratory results and clinical outcomes.ResultsOur study group comprised 435 (0.72%) of the 59 997 patients hospitalised during the study period. The mortality rate and mean hospital stays were significantly higher in the study group, and infectious diseases were the most common diagnoses, affecting 389 patients (89.4%), particularly pneumonia (47.1%). Higher CRP was correlated with low albumin levels (p < 0.01). Bacteraemia was the most prevalent diagnosis (38%) in the 84 oncology patients, with a crude mortality rate of 17.6%.ConclusionInfectious diseases, mainly bacterial, were the most common diagnoses in previously healthy children with CRP ≥30 mg/dL. Extremely elevated CRP levels were associated with an unfavourable clinical outcome, including high mortality, particularly in oncology patients. Paediatricians should be aware of the significance of extremely elevated CRP levels.
Changes in myonuclear domain size do not precede muscle hypertrophy during prolonged resistance‐type exercise training
Authors: Snijders T. , Smeets J. S. J. , van Kranenburg J. , Kies A. K. , van Loon L. J. C. , Verdijk L. B. 
Published: September 2015

AbstractAimMuscle fibre hypertrophy is accompanied by an increase in myonuclear number, an increase in myonuclear domain size or both. It has been suggested that increases in myonuclear domain size precede myonuclear accretion and subsequent muscle fibre hypertrophy during prolonged exercise training. In this study, we assessed the changes in muscle fibre size, myonuclear and satellite cell content throughout 12 weeks of resistance‐type exercise training in young men.MethodsTwenty‐two young men (23 ± 1 year) were assigned to a progressive, 12‐weeks resistance‐type exercise training programme (3 sessions per week). Muscle biopsies from the vastus lateralis muscle were taken before and after 2, 4, 8 and 12 weeks of exercise training. Muscle fibre size, myonuclear content, myonuclear domain size and satellite cell content were assessed by immunohistochemistry.ResultsType I and type II muscle fibre size increased gradually throughout the 12 weeks of training (type I: 18 ± 5%, type II: 41 ± 6%, P < 0.01). Myonuclear content increased significantly over time in both the type I (P < 0.01) and type II (P < 0.001) muscle fibres. No changes in type I and type II myonuclear domain size were observed at any time point throughout the intervention. Satellite cell content increased significantly over time in both type I and type II muscle fibres (P < 0.001).ConclusionIncreases in myonuclear domain size do not appear to drive myonuclear accretion and muscle fibre hypertrophy during prolonged resistance‐type exercise training in vivo in humans.
Adverse Drug Reactions for Medicines Newly Approved in Japan from 1999 to 2013: Hypertension and Hypotension
Authors: Nagayama Takashi , Nishida Minoru , Hizue Masanori , Ogino Yamato , Fujiyoshi Masato 
Published: September 2015

AbstractIn this survey, the correlation between adverse drug reactions (ADRs) in human and animal toxicities was investigated for 393 medicines which were approved in Japan from September 1999 to March 2013. ADRs were collected from each Japanese package insert. Comparable animal toxicities with ADRs were collected by thorough investigation of common technical documents. The results of this survey show that hypertension and/or hypotension were mainly observed in medicines affecting the central nervous system. Hypertension was also observed in antipyretics, analgesics, anti‐inflammatory agents, vasoconstrictors and agents using antibody. Concordance between human ADRs and animal toxicities was analysed. True‐positive rate for hypertension and hypotension is 0.29 and 0.52, respectively. Positive likelihood ratio and inverse negative likelihood ratio are 1.98 and 1.21, respectively, in hypertension and 1.67 and 1.44, respectively, in hypotension. Concordance between human ADRs and animal toxicities is not so high in hypertension and hypotension. Identified mechanisms as on‐target for hypertension and hypotension are 29.8% and 30.5%, respectively. More than half of the causative factors of hypertension and hypotension were unable to be elucidated. Our results show that the intake of medicines is often linked to blood pressure variations that are not predicted in animal toxicity studies. Improvement of drug development processes may be necessary to provide safer medicines because current animal toxicity studies are insufficient to predict all ADRs in human beings.
A new multi‐stage recession model for Proglacial Lake Humber during the retreat of the last British–Irish Ice Sheet
Authors: Fairburn William A. , Bateman Mark D. 
Published: September 2015

The single most prominent lake associated with the retreat phase of the last British–Irish Ice Sheet (BIIS) was Proglacial Lake Humber. The present research elucidates a revised regional history of Proglacial Lake Humber from its maximum elevation to its demise using a combination of landscape mapping and luminescence dating. The results of mapping multiple Lake Humber strandlines are now best described by an eight‐stage recessional model. Erosional highstands of the lake can be shown to post‐date the BIIS advance that deposited the Skipsea Till at around 17 ka whereas new OSL ages show that Lake Humber was nearing its demise by 15.5±0.8 ka, indicating a possible short‐lived lake. Multiple lake level stands are attributed to the switching of lake outlets from the Lincolnshire Gap to the Humber Gap and to oscillations of the BIIS blocking the latter on more than one occasion and subsequently at a lower elevation with till. The horizontal or near‐horizontal shorelines confirm that isostatic adjustment did not occur during the demise of Lake Humber, indicating that BIIS advances in the North Sea region and Vale of York were not only dynamic but of short duration.
The effect of cigarette smoking on early osseointegration of dental implants: a prospective controlled study
Authors: Bezerra Ferreira José Divino , Rodrigues Jose Augusto , Piattelli Adriano , Iezzi Giovanna , Gehrke Sergio Alexandre , Shibli Jamil Awad 
Published: September 2015

AbstractObjectiveThis study evaluated the effect of cigarette smoking on the percentage of early bone‐to‐implant contact (BIC%), the bone density in the threaded area (BA%) as well as the bone density outside the threaded area (BD%) around micro‐implants with sandblasted acid‐etched surface retrieved from human jaws.Material and methodsTwenty‐two subjects (mean age 55.4 ± 4.5 years) were divided in two groups: smokers (n = 11 subjects) and never‐smokers (n = 11 subjects). Each subject received one micro‐implant during conventional mandible or maxilla implant surgery. After 8 weeks, the micro‐implants and the surrounding tissue were removed and prepared for histomorphometric analysis.ResultsTwo micro‐implants placed in smokers showed no osseointegration. Early stages of maturation of the newly formed bone were present, mainly in the never‐smokers. Marginal bone loss, gap, and fibrous tissue were present around some implants retrieved from smokers. Histometric evaluation indicated that the meanBIC% ranged between 25.9 ± 9.1 and 39.8 ± 14.2 for smokers and non‐smokers, respectively (P = 0.02). Smokers presented 28.6 ± 10.1 ofBA% while never‐smokers showed 46.4 ± 18.8 (P = 0.04). The mean ofBD% ranged between 19.1 ± 7.6 and 28.5 ± 18.8 for smokers and never‐smokers, respectively (P = 0.21).ConclusionCigarette smoking has a detrimental effect on early bone tissue response around sandblasted acid‐etched implant surface topographies.
Intra‐operative neuromonitoring of the vagus nerve during thyroidectomy. A prospective study
Authors: Klopp‐Dutote N. , Biet‐Hornstein A. , Guillaume‐Souaid G. , Strunski V. , Page C. 
Published: September 2015

ObjectivesTo determine whether intra‐operative neuromonitoring (IONM) of the vagus nerve during thyroidectomy can predict postoperative vocal fold palsy.DesignA single‐centre, prospective study.SettingUniversity Hospital.ParticipantsA total of 95 patients underwent thyroid surgery. A total of 160 vagus nerves were studied. The amplitude of the action potential of vocal muscles was recorded intra‐operatively by indirect supramaximal stimulation of the vagus nerve. All patients underwent flexible fibre‐optic laryngoscopy on postoperative day 1 to detect the presence of vocal fold palsy.Main outcome measuresThe primary outcome measure was the difference of the action potential amplitude of the vagus nerve before and after resection of the thyroid lobe. Statistical analysis determined the amplitude variation cut‐off able to accurately predict postoperative vocal fold palsy.ResultsTransient vocal fold palsy was observed in 4.375% of cases, and permanent fold palsy was observed in 1.25% of cases. A decrease of the action potential amplitude by more than 61% was statistically significantly associated with postoperative vocal fold palsy. A greater than 87% decrease of the amplitude of the action potential was correlated with permanent postoperative vocal fold palsy.ConclusionIONM of the vagus nerve during thyroidectomy may accurately predict postoperative vocal fold palsy.
Schmerzen und Schmerztherapie in der Dermatologie
Authors: Beiteke Ulrike , Bigge Stefan , Reichenberger Christina , Gralow Ingrid 
Published: September 2015

ZusammenfassungEine Prävalenzrate von 23 Millionen Deutschen mit chronischen Schmerzen ist anzunehmen. In einer aktuellen Erhebung waren 30 % der chronischen Schmerzpatienten mit ihrer Schmerztherapie nicht zufrieden. Des Weiteren leiden fünf Millionen Deutsche an neuropathischen Schmerzen, wovon 20 % nicht ausreichend therapiert sind. Schmerz ist auch ein Symptom vieler dermatologischer Krankheitsbilder. Die zumeist somatischen Schmerzen sind vielfach als milde Schmerzen einzustufen. Eine zunehmende Forschung zur Lebensqualität zeigt jedoch eine deutliche Beeinträchtigung der Lebensqualität durch moderate Schmerzen, u.a. bei Psoriasis vulgaris et arthropathica. Starke Schmerzen treten bei Herpes zoster, Ulcus cruris und Pyoderma gangraenosum auf.Als Grundlagen werden Schmerzklassifikation und im kurzen Exzerpt Schmerzleitung und ‐modulation dargestellt. Der Einsatz standardisierter Skalen zur Erhebung und Verlaufsbeobachtung der Schmerzstärke wird empfohlen, um Therapieoptimierungen zu gewährleisten und interdisziplinär auf gleicher Basis zu kommunizieren. Die Weiterbildung in der Dermatologie sieht den Erwerb von Kenntnissen, Erfahrungen und Fertigkeiten in der allgemeinen Schmerztherapie vor. Bezogen darauf werden grundlegende Behandlungskonzepte in Anlehnung an das erweiterte WHO‐Schema, ein stufenweises Vorgehen sowie Kombinationstherapien dargestellt. Der Fokus dieser Arbeit liegt auf der Schmerztherapie o. g. konservativ zu behandelnder stark schmerzhafter Dermatosen. Neben gängigen Therapeutika und aktuellen Therapiestandards werden, soweit vorhanden, leitlinienbasiert spezifische Optionen erörtert. Der Wissensstand zum peri‐ und postoperativen Schmerzmanagement wird kurz umrissen. Dieser Artikel vermittelt:

▸ Grundlagen zur Klassifikation und Neurophysiologie von Schmerzen,
▸ Standards für die Schmerzdokumentation bei Kindern und Erwachsenen,
▸ allgemeine Standards für eine medikamentöse Schmerztherapie,
▸ aktuelle spezifische Therapieoptionen für Zosterneuralgie, Ulcus cruris, Pyoderma gangraenosum im Zusammenhang mit dem erweiterten WHO‐Schema.