bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergence of visual and whisker responses in the primary somatosensory thalamus (ventral posterior medial region) of the mouse
Authors: Allen Annette E , Procyk Christopher A. , Brown Timothy M. , Lucas Robert J. 
Published: August 2016

Key points
Using in vivo electrophysiology, we find that a subset of whisker‐responsive neurons in the ventral posterior medial region (VPM) respond to visual stimuli.
These light‐responsive neurons in the VPM are particularly sensitive to optic flow.
Presentation of optic flow stimuli modulates the amplitude of concurrent whisker responses.
Visual information reaches the VPM via a circuit encompassing the visual cortex.
These data represent a new example of cross‐modal integration in the primary sensory thalamus.
AbstractSensory signals reach the cortex via sense‐specific thalamic nuclei. Here we report that neurons in the primary sensory thalamus of the mouse vibrissal system (the ventral posterior medial region; VPM) can be excited by visual as well as whisker stimuli. Using extracellular electrophysiological recordings from anaesthetized mice we first show that simple light steps can excite a subset of VPM neurons. We then test the ability of the VPM to respond to spatial patterns and show that many units are excited by visual motion in a direction‐selective manner. Coherent movement of multiple objects (an artificial recreation of ‘optic flow’ that would usually occur during head rotations or body movements) best engages this visual motion response. We next show that, when co‐applied with visual stimuli, the magnitude of responses to whisker deflections is highest in the presence of optic flow going in the opposite direction. Importantly, whisker response amplitude is also modulated by presentation of a movie recreating the mouse's visual experience during natural exploratory behaviour. We finally present functional and anatomical data indicating a functional connection (probably multisynaptic) from the primary visual cortex to VPM. These data provide a rare example of multisensory integration occurring at the level of the sensory thalamus, and provide evidence for dynamic regulation of whisker responses according to visual experience.
Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)
Authors: Li Xuewei , Kui Ling , Zhang Jing , Xie Yinpeng , Wang Liping , Yan Yan , Wang Na , Xu Jidi , Li Cuiying , Wang Wen , van Nocker Steve , Dong Yang , Ma Fengwang , Guan Qingmei 
Published: August 2016

Abstract

Background
Domesticated apple (Malus × domestica Borkh) is a popular temperate fruit with high nutrient levels and diverse flavors. In 2012, global apple production accounted for at least one tenth of all harvested fruits. A high-quality apple genome assembly is crucial for the selection and breeding of new cultivars. Currently, a single reference genome is available for apple, assembled from 16.9 × genome coverage short reads via Sanger and 454 sequencing technologies. Although a useful resource, this assembly covers only ~89 % of the non-repetitive portion of the genome, and has a relatively short (16.7 kb) contig N50 length. These downsides make it difficult to apply this reference in transcriptive or whole-genome re-sequencing analyses.

Findings
Here we present an improved hybrid de novo genomic assembly of apple (Golden Delicious), which was obtained from 76 Gb (~102 × genome coverage) Illumina HiSeq data and 21.7 Gb (~29 × genome coverage) PacBio data. The final draft genome is approximately 632.4 Mb, representing ~ 90 % of the estimated genome. The contig N50 size is 111,619 bp, representing a 7 fold improvement. Further annotation analyses predicted 53,922 protein-coding genes and 2,765 non-coding RNA genes.

Conclusions
The new apple genome assembly will serve as a valuable resource for investigating complex apple traits at the genomic level. It is not only suitable for genome editing and gene cloning, but also for RNA-seq and whole-genome re-sequencing studies.
Features and Outcome of Autonomous Thyroid Nodules in Children: 31 Consecutive Patients Seen at a Single Center
Authors: Ly Samantha , Frates Mary C. , Benson Carol B. , Peters Hope E. , Grant Frederick D. , Drubach Laura A. , Voss Stephan D. , Feldman Henry A. , Smith Jessica R. , Barletta Justine , Hollowell Monica , Cibas Edmund S. , Moore Francis D. , Modi Biren , Shamberger Robert C. , Huang Stephen A. 
Published: August 2016

Context:Most thyroid nodules are benign and their accurate identification can avoid unnecessary procedures. In adult patients, documentation of nodule autonomy is accepted as reassurance of benign histology and as justification to forgo biopsy or thyroidectomy. In contrast, the negative predictive value of nodule autonomy in children is uncertain. Some recent publications recommend surgical resection as initial management, but few address the degree of TSH suppression or the specific scintigraphic criteria used to diagnose autonomy.Objective:The objective of the study was to study the presenting features and cancer risk of children with autonomous nodules.Design and Setting:Medical records of all 31 children diagnosed with autonomous nodules at our center from 2003 to 2014 were retrospectively reviewed.Patients and Results:All children met full diagnostic criteria for autonomous nodules, defined by both autonomous 123I uptake into the nodule and the suppression of uptake in the normal thyroid parenchyma on scintigraphy performed during hypothyrotropinemia. The median age of presentation was 15 years (range 3–18 y) with a female to male ratio of 15:1. Fifty-eight percent of patients had solitary nodules and 42% had multiple nodules. The median size of each patient’s largest autonomous nodule was 39 mm (range 18–67 mm). Most of the children in this series (68%) had diagnostic biopsies and/or operative pathology of their largest autonomous nodule, which showed benign cytology or histology in all cases.Conclusions:In this pediatric series, the cancer rate observed in biopsied or resected autonomous nodules was 0%. Whereas larger studies are needed to confirm our findings, these results agree with earlier reports suggesting that thyroid cancer is rare in rigorously defined autonomous nodules and support that conservative management may be offered to selected children who meet strict diagnostic criteria for autonomous nodules, deferring definitive therapies until adulthood when the risks of thyroidectomy and 131I ablation are lower.
Genezis of Self-Government
Authors: Латфуллин  , Latfullin Gennadiy 
Published: August 2016

The self-government today is a qualitatively new phenomenon, which preserved just the old name in the new
conditions of privatization of property and privatization of enterprises, the rapid development of its private
form, as relevant part of measures for transition to market relations. Self-government as a phenomenon of
social life has always been, what stages of development the society was. Externally, self-governing relations
were presented in different forms, which suggest that in the differences in the forms it is necessary to see
the uniformity of nature. In different nations in different countries, and in the same nation in different historical
periods, there were different social roles of subjects and objects of management and government, and their
social, ethical and legal status, and, therefore, relations with state authorities and management.
Molecular models of human visual pigments: insight into the atomic bases of spectral tuning
Authors: Centola Francesca , Polticelli Fabio 
Published: August 2016

Abstract
The cycle of vision is a chain of biochemical reactions that occur after exposure of the pigments to the light. The known mechanisms of the transduction of the light pulse derive mainly from studies on bovine rhodopsin. The objective of this work is to construct molecular models of human rhodopsin and opsins, for which three-dimensional structures are not available, to analyze the retinal environment and identify the similarities and differences that characterize the human visual pigments. One of the main results of this work is the identification of Glu102 as the probable second counterion of the Schiff base in M opsin (green pigments) and L opsin (red pigments). Further, the analysis of the molecular models allows uncovering the molecular bases of the different absorption maxima of M and L opsins with respect to rhodopsin and S opsin. These differences appear to be due to both an increase in the polarity of the retinal environment and specific electrostatic interactions, which determine a reorganization of the electronic distribution of retinal by selectively stabilizing one of the two resonance forms.
Σχολαστικός. Remarques sur le sens du terme à Byzance (IVe–XVe siècles)
Authors: Loukaki Marina 
Published: August 2016

Abstract
The Greek word scholastikos as a human attribute appears continuously from classical antiquity to modern times. However, over the centuries, the term took various nuances, which are associated with respective activities, the participation in public life and the social status of the persons qualified as scholastikoi. In the article, starting with Axel Claus’ conclusions in his doctoral thesis (Cologne 1965) as well as the exploitation of new evidences concludes that from the 3rd until the 7th century AD the number of people known as scholastikoi is particularly high. These people were well educated with rhetoric and legal knowledge. The term did not designate a specific profession, though often during this period a scholastikos gathered the characteristics of a jurist in today’s sense; he was an advocate, legal advisor, teacher of law, judge, notary, etc. Although he was not directly related to the education system as a teacher or professor of rhetoric, occasionally a scholastikos could have been, under certain circumstances, a private teacher of grammar (grammarian). During the middle and late Byzantine period, the attribute scholastikos for a person is found in very few and isolated cases (Arethas’ letters to Niketas David Paphlagon, Ecloga privata aucta, Alexiad, Nikephoros Gregoras to Theodoros Metochites and Thomas Magistros, Life of saint Athanasios of Meteora). It is clear that scholastikos, as a human type with the characteristics outlined above, did not disappear, but the term was no longer used in this context. According to the rare available evidence, most of the authors used the term in its ancient Greek meaning, associating it mainly with education, teachers and letters in general.
Il Manoscritto Plut. 86.14 della Biblioteca Medicea Laurenziana di Firenze
Authors: Rapisarda Stefano , Calcagno Agata 
Published: August 2016

Abstract
The manuscript Plut. 86.14 displays an uncommon variety of geomantical texts in medieval Greek.We propose to challenge the traditional idea of the ‘derivation’ of Greek geomancy from the Arabic one, and to show the existence of an ‘original’ Greek tradition, quite divergent from the Arabic one for what concerns both the technical lexicon and the procedures of interrogation.
Teaching Greek grammar in 11th-century Constantinople: Michael Psellus on the Greek ‘dialects’
Authors: Van Rooy Raf 
Published: August 2016

Abstract
In this paper, I aim at sketching the place of the Ancient Greek literary dialects within grammar in the 11th-century Byzantine curriculum, for which a didactic grammatical poem, composed by the polymath Michael Psellus (ca. 1018-ca. 1080), is a unique and understudied source (viz. Poemata, 6). I do so by offering, together with a first English translation of the relevant verses, a close analysis of part of the poem and its sources. This enables us to assess how Psellus pictured the relationship of the κοινή (koinè) with the four other canonical dialects. I likewise argue that, although Psellus does not offer a definition of the word διάλεκτος (dialektos), his poem nevertheless allows us to reconstruct his conception of it to a certain extent. This contribution also seeks to contextualize Psellus’ views against the backdrop of the Hellenistic and Byzantine tradition of Greek dialect studies.
Der Zusammenhang von Urbanität und Literatur bei Dante
Authors: Klinkert Thomas 
Published: August 2016

Riassunto
Lo scopo di questo contributo è di analizzare il rapporto tra urbanità e letteratura sulla base dell’esempio di Dante. Il punto di partenza dell’argomentazione è il celebre affresco di Domenico di Michelino (1465), che raffigura la Commedia quale atto di comunicazione rivolto a Firenze, suo destinatario privilegiato. Quest’interpretazione del pittore tocca il cuore dell’opera dantesca, come si cerca di mostrare tramite l’analisi di due canti (Inf. VI e Inf. X). Risulta da quest’analisi che la Commedia può essere considerata il correlato testuale di un ordine del sapere che nasce nell’ambito dello sviluppo sociale, culturale e politico della città di Firenze dei secoli XIII e XIV. All’interno della Commedia si manifestano delle contraddizioni fondamentali. Da una parte, infatti, Dante critica esplicitamente e radicalmente la mentalità affaristica dei fiorentini e le loro discordie politiche; ma dall’altra parte egli è consapevole di dover molto al milieu innovativo di questa città in quanto poeta e pensatore filosofico. Inoltre si cerca di mostrare che il testo dantesco in parte presuppone un lettore che conosca bene dall’interno la situazione di Firenze. Così la dimensione urbana è integrata nella Commedia non solo a livello tematico, ma soprattutto a livello strutturale.
The use of objective oriented project planning tools for nanosafety and health concerns: a case study in nanomedicine research project
Authors: Nejadmoghaddam Mohammad-Reza , Babamahmoodi Abdolreza , Minai-Tehrani Arash , Zarnani Amir-Hassan , Dinarvand Rassoul 
Published: August 2016

AbstractPotential human health and environmental risks associated with nanoscience research projects and their deliverables, termed nanosafety, is one of the important issues for translating research findings into commercially viable products. This paper examined the applicability of project management tools to address nanosafety in an efficient manner. Using objectives oriented project planning (OOPP) we describe a new integrated content of the problem tree, the result tree, and the logical framework approach (LFA), by modeling our nanomedicine research project entitled “Nanomedicine preparation based on antibody drug conjugate (ADC)” as a case study. As a main result of the case study, we demonstrated an LFA matrix that highlights the need to deal with nanosafety as an activity of the research project. Consequently, the activity can lead to the output, standing operating procedure (SOP), for managing the project waste disposals and its deliverables side effects. In general, such output can be concluded as an important output for all nanoscience research projects to avoid underestimating risks for their nano-objects. Moreover, this article is written in the hope of providing an easy-to-understand template of project management tools for novice nanomedicine researchers who aim to apply OOPP in the design of their research projects.
Estimation of the Overall Treatment Effect in the Presence of Interference in Cluster-Randomized Trials of Infectious Disease Prevention
Authors: Carnegie Nicole Bohme , Wang Rui , De Gruttola Victor 
Published: August 2016

AbstractAn issue that remains challenging in the field of causal inference is how to relax the assumption of no interference between units. Interference occurs when the treatment of one unit can affect the outcome of another, a situation which is likely to arise with outcomes that may depend on social interactions, such as occurrence of infectious disease. Existing methods to accommodate interference largely depend upon an assumption of “partial interference” – interference only within identifiable groups but not among them. There remains a considerable need for development of methods that allow further relaxation of the no-interference assumption. This paper focuses on an estimand that is the difference in the outcome that one would observe if the treatment were provided to all clusters compared to that outcome if treatment were provided to none – referred as the overall treatment effect. In trials of infectious disease prevention, the randomized treatment effect estimate will be attenuated relative to this overall treatment effect if a fraction of the exposures in the treatment clusters come from individuals who are outside these clusters. This source of interference – contacts sufficient for transmission that are with treated clusters – is potentially measurable. In this manuscript, we leverage epidemic models to infer the way in which a given level of interference affects the incidence of infection in clusters. This leads naturally to an estimator of the overall treatment effect that is easily implemented using existing software.
Complementary and alternative medicine for rheumatic diseases
Authors: Teng Sophia 
Published: August 2016

Abstract
The use of complementary and alternative medicine is not uncommonly encountered in our patients. This manuscript reviewed the latest evidence on other modalities in treating rheumatic diseases. Treatments that are found to be helpful for rheumatoid arthritis include herbs, fish oil, and acupuncture. Fish oil, vitamin D, N-acetylcysteine, and cognitive behavior treatments are helpful for systemic lupus erythematosus. Hydrotherapy and massage are potentially beneficial for fibromyalgia patients. Diet supplement is not found to be beneficial for osteoarthritis. CAM modalities will need further studies.
Semiparametric Regression Estimation for Recurrent Event Data with Errors in Covariates under Informative Censoring
Authors: Yu Hsiang , Cheng Yu-Jen , Wang Ching-Yun 
Published: August 2016

Abstract
Recurrent event data arise frequently in many longitudinal follow-up studies. Hence, evaluating covariate effects on the rates of occurrence of such events is commonly of interest. Examples include repeated hospitalizations, recurrent infections of HIV, and tumor recurrences. In this article, we consider semiparametric regression methods for the occurrence rate function of recurrent events when the covariates may be measured with errors. In contrast to the existing works, in our case the conventional assumption of independent censoring is violated since the recurrent event process is interrupted by some correlated events, which is called informative drop-out. Further, some covariates may be measured with errors. To accommodate for both informative censoring and measurement error, the occurrence of recurrent events is modelled through an unspecified frailty distribution and accompanied with a classical measurement error model. We propose two corrected approaches based on different ideas, and we show that they are numerically identical when estimating the regression parameters. The asymptotic properties of the proposed estimators are established, and the finite sample performance is examined via simulations. The proposed methods are applied to the Nutritional Prevention of Cancer trial for assessing the effect of the plasma selenium treatment on the recurrence of squamous cell carcinoma.
Die Interpretation des p-Wertes – Grundsätzliche Missverständnisse
Authors: Hirschauer Norbert , Mußhoff Oliver , Grüner Sven , Frey Ulrich , Theesfeld Insa , Wagner Peter 
Published: August 2016

Zusammenfassung
Der p-Wert wird vielfach als Goldstandard für Inferenzschlüsse angesehen. Zur Validierung statistischer Zusammenhänge hat sich die Konvention herausgebildet, möglichst geringe p-Werte einzufordern und bei Werten unterhalb gewisser Schwellen (z. B. 0,05) von statistisch signifikanten Ergebnissen zu sprechen. Häufig wird der p-Wert auch als Irrtumswahrscheinlichkeit bezeichnet. Beide Begriffe sind problematisch, da sie Missverständnissen Vorschub leisten. Hinzu kommt, dass das sog. p-hacking, d. h. die gezielte Suche nach Auswertungen, die zu statistisch signifikanten Ergebnissen führen, Verzerrungen hervorrufen und die Rate falscher Entdeckungen (false discovery rate) erhöhen kann. Fehlinterpretationen des p-Wertes und auswertungsbedingte Verzerrungen wurden über die Jahrzehnte hinweg immer wieder kritisch diskutiert. In der empirischen Forschung scheinen sie aber persistent zu sein und in den letzten Jahren wurde die p-Wert-Debatte wegen der Nicht-Reproduzierbarkeit vieler Studien zunehmend intensiv geführt. Angesichts der über die Disziplinen verstreuten und oft auf Einzelaspekte abzielenden Literatur zur p-Wert-Problematik beschreibt dieser Methodenkommentar systematisch die wichtigsten Probleme und diskutiert die entsprechenden Lösungsvorschläge.
Analyzing the Full BINMA Time Series Process Using a Robust GQL Approach
Authors: Khan Naushad Mamode , Sunecher Yuvraj , Jowaheer Vandna 
Published: August 2016

AbstractWe investigate a new bivariate-integer valued moving average time series process where the innovation series follow the bivariate Poisson assumption under stationary moments and constant cross-correlations. Furthermore, due to the complication involved in specifying the joint likelihood function, this paper considers a robust generalized quasi-likelihood approach to estimate the mean, serial and dependence parameters. Unlike previous estimation techniques such as the Generalized Least Squares, this estimation approach here involves a two-step Newton-Raphson iterative procedure where in the first step, the serial and cross correlations are estimated while in the second step, these dependence estimates are used to compute iteratively the vector of regression coefficients. The consistency of the estimates under this approach is checked through several simulation experiments under different combinations of low and high serial and cross-correlations.
Zirkulierende Nukleinsäuren – ein neues Universum in der laboratoriumsmedizinischen Diagnostik
Authors: Neumaier Michael 
Published: August 2016

Zusammenfassung:
Zirkulierende zell-freie Nukleinsäuren (cfNA, meist als cfDNA bezeichnet) werden zunehmend als eine neue Klasse von diagnostischen Markern wahrgenommen. DNA, mRNA und miRNA zirkulieren weniger in „nackter Form“, sondern sind verpackt und entgehen so einem schnellen Abbau im peripheren Blut. Zusammen mit der Tatsache, dass cfNA in verschiedenen wichtigen Erkrankungen sowohl qualitativ als auch quantitativ verändert sind, schafft dies ein völlig neues Universum für die labormedizinische Diagnostik. Erste Anwendungen wie z.B. die sensitive und spezifische Detektion von tumor-spezifischen Mutationen im Plasma erobern die Arena der labordiagnostischen Krankenversorgung und erlauben den Nachweis therapeutisch relevanter molekulargenetischer Tumorprofile aus dem Blut für die frühe Erkennung von Rezidiv oder Therapieversagen. Es bleiben viele Fragen zu klären, darunter die Kreuzvalidierung mit etablierten und wichtigen Parametern der Labormedizin. Auch die Einordnung präanalytischer Aspekte, die metrologische Fragen von Richtigkeit und Präzision, etc. sind für die Einordnung von analytischer und medizinischer Qualität dringend erforderlich. Nicht zuletzt eröffnen die frei zirkulierenden Nukleinsäuren eine völlig neue Biologie von Signalen, die in Gesundheit und Krankheit zwischen Zellen und Organen durch unseren Körper reisen. Es wird eine große wissenschaftliche Herausforderung sein, die biochemischen und pathobiochemischen Implikationen zu verstehen. Für Entwicklung und Implementation dieses neuen diagnostischen Felds ist signifikant, dass die Klinische Chemie die erforderlichen Expertisen sowie das komplementierende Spektrum etablierter Biomarker bereithält, um eine ordentliche Transition des Einsatzes zirkulierender Nukleinsäuren in die Diagnostik zu gewährleisten. Dies wird vorhersehbar das Spektrum der Labormedizin komplementieren, um die therapeutische Medizin bei ihren Entscheidungen in der Patientenbehandlung zu unterstützen.