bluuebunny/crossref_metadata_2025_split huggingface dataset:
MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format
Authors: Ahmed Zeeshan , Dandekar Thomas 
Published: December 2015

Published scientific literature contains millions of figures, including information about the results obtained from different scientific experiments e.g. PCR-ELISA data, microarray analysis, gel electrophoresis, mass spectrometry data, DNA/RNA sequencing, diagnostic imaging (CT/MRI and ultrasound scans), and medicinal imaging like electroencephalography (EEG), magnetoencephalography (MEG), echocardiography (ECG), positron-emission tomography (PET) images. The importance of biomedical figures has been widely recognized in scientific and medicine communities, as they play a vital role in providing major original data, experimental and computational results in concise form. One major challenge for implementing a system for scientific literature analysis is extracting and analyzing text and figures from published PDF files by physical and logical document analysis. Here we present a product line architecture based bioinformatics tool ‘Mining Scientific Literature (MSL)’, which supports the extraction of text and images by interpreting all kinds of published PDF files using advanced data mining and image processing techniques. It provides modules for the marginalization of extracted text based on different coordinates and keywords, visualization of extracted figures and extraction of embedded text from all kinds of biological and biomedical figures using applied Optimal Character Recognition (OCR). Moreover, for further analysis and usage, it generates the system’s output in different formats including text, PDF, XML and images files. Hence, MSL is an easy to install and use analysis tool to interpret published scientific literature in PDF format.
High pre-transplant TREC levels indicate good prognosis after hematopoietic stem cell transplantation
Authors: de Moraes Arantes Adriano , Kawemura Kharen , Seber Adriana , Rodrigues de Oliveira José Salvador , Gerbase-DeLima Maria , Shulzhenko Natalia , Morgun Andrey 
Published: December 2015

BackgroundThymus-dependent T-cell reconstitution plays a role in immune recovery after stem cell transplantation (HSCT). High pre-HCST thymic function has been associated with higher survival, lower incidence of acute and chronic graft versus host disease (GVHD) and lower incidence of infections. The aim of this study was to analyze the relationship between pre-HSCT peripheral blood levels of T-cell receptor excision circles (TREC) and post-HSCT clinical events in recipients of HLA-identical hematopoietic stem cell transplants.MethodDelta deletion signal joint TRECs (sjTRECs) formed by the dREC-yJa rearrangement were quantified by real time PCR in peripheral blood lymphocytes of 62 HSCT recipients.ResultsUnivariate analysis revealed an association between low TREC levels and a higher incidence of grade II-IV acute GVHD (p=0.026), bacterial infection (p=0.005) and cytomegalovirus infection (p=0.033), whereas high TREC levels were associated with higher overall survival (p=0.028). In the multivariate analysis, low pre-HSCT TREC levels remained independently associated with lower survival (p=0.032; RR 2.6), occurrence of grade II-IV acute GVHD (p=0.031; RR: 2.5), bacterial infection (p=0.006, RR: 6.6) and cytomegalovirus infection (p=0.039; RR:2.8).ConclusionOur results corroborate the concept that pre-HSCT recipient´s thymic function is an important predictor of risk for acute grade II-IV GVHD and infection.
Biotic homogenization and differentiation
in weed vegetation over the last 70 years
Authors: Šilc Urban 
Published: December 2015

Abstract
Biotic homogenization is the increasing similarity
of the species composition of communities over time and
represents a loss of biodiversity. We analysed changes in
weed vegetation over a period of 70 years by comparing
three datasets (from 1939, 2002 and 2012) sampled with
the same methodology. We present the results of changes
in species richness, homogenization and differentiation as
expanding neophytes and generalist species. The species
richness of weed communities decreased and the number
of neophytes in cereal fields and root crops increased
over time. The decreased ratio of specialists to generalists
in vernal communities and cereal crops indicates
homogenization, while the ratio of generalists to specialists
increased in root crops.
The CLU-files: disentanglement of a mystery
Authors: Rohne Philipp , Prochnow Hans , Koch-Brandt Claudia 
Published: December 2015

AbstractThe multifaceted protein clusterin (CLU) has been challenging researchers for more than 35 years. The characterization of CLU as a molecular chaperone was one of the major breakthroughs in CLU research. Today, secretory clusterin (sCLU), also known as apolipoprotein J (apoJ), is considered one of the most important extracellular chaperones ever found. It is involved in a broad range of physiological and pathophysiological functions, where it exerts a cytoprotective role. Descriptions of various forms of intracellular CLU have led to further and even contradictory functions. To untangle the current state of knowledge of CLU, this review will combine old views in the field, with new discoveries to highlight the nature and function of this fascinating protein(s). In this review, we further describe the expression and subcellular location of various CLU forms. Moreover, we discuss recent insights into the structure of CLU and assess how structural properties as well as the redox environment determine the chaperone activity of CLU. Eventually, the review connects the biochemistry and molecular cell biology of CLU with medical aspects, to formulate a hypothesis of a CLU function in health and disease.
The emergence of disjunction: A history of constructionalization in Chinese
Authors: Jing-Schmidt Zhuo , Peng Xinjia 
Published: December 2015

AbstractThis study investigates the diachronic development of Chinese disjunction, drawing implications both for principles of diachronic Construction Grammar, and for the linguistic typology of disjunction. Close examinations of data from historical corpora revealed non-linear, gradual constructional changes based on complex yet principled interactions of conceptual origin, constructional patterning, discourse pragmatics, and an isolating typology in the development of Chinese disjunction. Specifically, the results (1) show that construction is the source, unit and product of change, (2) demonstrate the pivotal role of syntactic and semantic reanalysis in the micro changes leading to the constructionalization of disjunction, (3) reveal a conceptual and diachronic continuity between epistemic uncertainty and disjunction, (4) highlight frequency of use as a driving force in the conventionalization and entrenchment of constructional schema, and (5) confirm the role played by an isolating typology in syntactic and categorial reassignment as a key step in grammatical constructionalization.
Multivariate verification for sybil attack detection in VANET
Authors: Grover Jyoti , Gaur Manoj Singh , Laxmi Vijay 
Published: December 2015

Abstract
Wireless vehicular communication is used to enhance
traffic safety and to minimize congestion, thereby
leading to increased driving efficiency. A malicious node
can transmit an inaccurate message to trigger inevitable
situations by pretending to be multiple (other) vehicles.
Therefore, it is critical to identify malicious nodes as well
as fake messages generated by such nodes, and discard
such messages quickly. In a Sybil attack, an attacker participates
in the network with multiple forged identities in
order to disrupt the fundamental operations of VANET.
Sybil attacks are particularly easy to launch in VANETs
due to the open and broadcast nature of communication
medium. In this paper, we present the implementation of
simulated Sybil attack scenario in VANET and its consequences
on the performance of the network. We also propose
a lightweight, scalable and distributed detection approach
based on the difference in movement patterns of
Sybil nodes and legitimate nodes. In our approach, each
Road Side Unit (RSU) computes, stores and verifies various
parameter values including RSS, distance, angle of
passing-by vehicles through passive overhearing process
to detect Sybil attackers. The combination of different parameters
makes our detection approach highly accurate.
We validate our results on realistic traces obtained from
a multi-agent microscopic traffic simulator (MMTS). Simulation
results show the effectiveness of the proposed approach
to locate Sybil nodes with a different number of network
parameters.
Some Exploitation Properties of Wood Plastic Hybrid Composites Based on Polypropylene and Plywood Production Waste
Authors: Kajaks Janis , Kalnins Karlis , Uzulis Sandris , Matvejs Juris 
Published: December 2015

AbstractDuring the last 20–30 years many researchers have paid attention to the studies of properties of thewood polymer composites (WPC). A lot of works are closely related to investigations of exploitation properties of wood fibres or wood flour containing polyolefine composites [1, 2]. The most useful from wide selection of polyolefines are polypropylenes, but timber industry waste materials comprising lignocellulose fibres are often used as reinforcement of WPC [3–12]. Plywood industry is not an exception – part of waste materials (by-products) are used for heat energy, i.e. burned. In this work we have approbated reinforcing of polypropylene (PP) with one of the plywood industry by-products, such as birch plywood sawdust (PSWD),which containswood fibre fractions with different length [13]. The main fraction (50%) includes fibres with length l = 0.5 − 1 mm. Our previous study [13] has confirmed that PSWD is a promising filler for PP reinforcing. Addition of PSWD up to 40–50 wt.% has increased WPC tensile and flexural modulus, but decreased deformation ability of PP matrix, impact strength, water resistance and fluidity of composite melts. It was shown [13] that modification of the composites with interfacial modifier – coupling agent maleated polypropylene (MAPP content up to 5–7 wt.%) considerably improved all the abovementioned properties. SEM investigations also confirmed positive action of coupling agent on strengthening of adhesion interaction between components wood and PP matrix. Another way how to make better properties of the WPC is to form hybridcomposites [1, 14–24]. Very popular WPC modifiers are nanoparticle additions like organonanoclays, which increase WPC physical-mechanical properties - microhardness, water resistance and diminish barrier properties and combustibility [1, 2, 14–17, 19, 20]. The goal of this study was to investigate organonanoclays influence on plywood production industry by-product birch plywood sawdust (PSWD) containing polypropylenewood hybrid composites (WPHC) physical-mechanical and other exploitation properties.
Antinociceptive effects of dexmedetomidine via spinal substance P and CGRP
Authors: Li Ruiqin , Qi Feng , Zhang Junlong , Ji Yong , Zhang Dengxin , Shen Zhiyun , Lei Weifu 
Published: December 2015

Abstract
The aim of this study was to examine the role played by substance P and calcitonin gene-related peptide (CGRP)
within the dorsal horn of the spinal cord in engagement of antinociception evoked by dexmedetomidine (DEX).
Paw withdrawal threshold (PWT) to mechanical stimulation was determined after chronic intrathecal infusion of
DEX and enzyme-linked immunosorbent assay (ELISA) was employed to examine the levels of spinal substance
P and CGRP. Our results show that PWT was significantly increased by intrathecal administration of DEX in rats
(P < 0.05 vs. vehicle control, n = 20 in each group). Also, intrathecal infusion of DEX significantly decreased the
concentrations of substance P and CGRP as compared with vehicle control (P < 0.05 DEX vs. vehicle control,
n = 20 in each group). Blocking α2-adrenoreceptors (α2-AR) blunted the decreases of substance P and CGRP levels
and the enhancement of PWT evoked by DEX. Additionally, a linear relationship was observed between PWT and
the levels of spinal substance P (r = 0.87; P < 0.005) and CGRP (r = 0.85; P < 0.005). Moreover, blocking individual
substance P and CGRP receptors amplified PWT without altering substance P and CGRP levels. Thus, DEX plays a
role in stimulating α2-AR receptors, which thereby decreases substance P and CGRP levels within the dorsal horn.
This contributes to DEX-evoked antinociception.
Nanoscale organization and dynamics of the siglec CD22 cooperate with the cytoskeleton in restraining BCR signalling
Authors: Gasparrini Francesca , Feest Christoph , Bruckbauer Andreas , Mattila Pieta K , Müller Jennifer , Nitschke Lars , Bray Dennis , Batista Facundo D 
Published: December 2015

AbstractReceptor organization and dynamics at the cell membrane are important factors of signal transduction regulation. Using super‐resolution microscopy and single‐particle tracking, we show how the negative coreceptor CD22 works with the cortical cytoskeleton in restraining BCR signalling. In naïve B cells, we found endogenous CD22 to be highly mobile and organized into nanodomains. The landscape of CD22 and its lateral diffusion were perturbed either in the absence of CD45 or when the CD22 lectin domain was mutated. To understand how a relatively low number of CD22 molecules can keep BCR signalling in check, we generated Brownian dynamic simulations and supported them with ex vivo experiments. This combined approach suggests that the inhibitory function of CD22 is influenced by its nanoscale organization and is ensured by its fast diffusion enabling a “global BCR surveillance” at the plasma membrane.
A nontargeted study of muscle proteome in severely obese women with androgen excess compared with severely obese men and nonhyperandrogenic women
Authors: Insenser María , Montes-Nieto Rafael , Martínez-García M Ángeles , Escobar-Morreale Héctor F 
Published: December 2015

ObjectiveAndrogen excess in women is frequently associated with muscle insulin resistance, especially in obese women with polycystic ovary syndrome. However, whether this is a primary event or the result of indirect mechanisms is currently debated.DesignThis is an observational study.MethodsWe obtained skeletal muscle biopsies during bariatric surgery from severely obese men (n=6) and women with (n=5) or without (n=5) androgen excess. We used two-dimensional differential gel electrophoresis and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight mass spectrometry to identify muscle proteins showing differences in abundance between the groups of obese subjects.ResultsWomen with hyperandrogenism presented the lowest abundances of glycogen phosphorylase, pyruvate kinase, β-enolase, glycerol-3-phosphate dehydrogenase, creatine kinase M-type, and desmin, whereas the abundances of these molecules were similar in control women and men.ConclusionAccording to our nontargeted proteomic approach, women with hyperandrogenism show a specific alteration of the skeletal muscle proteome that could contribute to their insulin resistance. Because men do not show similar results, this alteration does not appear to be the direct effect on muscle of androgen excess, but rather the consequence of indirect mechanisms that merit further studies.
Compensatory function of the remaining testis is dissociated in boys and adolescents with monorchidism
Authors: Grinspon Romina P , Habib Carolina , Bedecarrás Patricia , Gottlieb Silvia , Rey Rodolfo A 
Published: December 2015

ObjectiveCompensatory hypertrophy has been classically described in patients with monorchidism. However, it remains unclear whether there is a functional compensatory activity of the different cell populations. Our aim was to assess the functional capacity of the solitary testis in monorchid males from infancy through puberty in order to determine whether the remaining gonad is capable of compensating the functional activity of Sertoli and Leydig cells of the absent gonad.DesignIn a retrospective, cross-sectional, analytical study performed at a tertiary paediatric public hospital, we included 89 boys with monorchidism and 358 healthy controls, aged 6 months–18 years. Testicular volume and circulating levels of reproductive hormones were compared between patients with monorchidism and normal boys. Serum anti-Müllerian hormone (AMH) and FSH were used as biomarkers of the functional mass of prepubertal Sertoli cells, whereas serum testosterone and LH were used as biomarkers of Leydig cells.ResultsIn the vast majority of the cases, the testicular volume of monorchid boys was smaller than the sum of the volume of both testes of healthy controls. Serum AMH was lower and FSH was higher in patients with monorchidism than in controls aged <3 and >13 years. Serum testosterone and LH did not differ significantly between patients and controls.ConclusionIn boys and adolescents with monorchidism, there is a dissociated capacity of the remaining testis to compensate for the absence of the other gonad: while Leydig cell function is largely compensated, Sertoli cell proliferation and function was lower than in controls.
A Comparison of Strategies for Retinopathy of Prematurity Detection
Authors: Kemper Alex R. , Prosser Lisa A. , Wade Kelly C. , Repka Michael X. , Ying Gui-shuang , Baumritter Agnieshka , Quinn Graham E. ,   for the e-ROP Study Cooperative Group
Published: December 2015

BACKGROUND AND OBJECTIVES:Delayed detection of type 1 retinopathy of prematurity (ROP) can lead to permanent visual impairment. Providing ROP examinations is challenging because of the limited ophthalmology workforce. This study compares digital imaging–based ROP detection strategies versus serial ROP examinations.METHODS:We conducted an individual-level microsimulation studyof a hypothetical cohort of 650 infants with gestational age from 23 to 30 weeks. Infants were evaluated by using strategies based on indirect ophthalmoscopy or digital imaging beginning at 32 weeks’ postmenstrual age (PMA) and continuing to discharge, transfer, or 40 weeks’ PMA. ROP status and the accuracy of digital imaging were based on the e-ROP (Telemedicine Approaches to Evaluating Acute-Phase ROP) study, which enrolled high-risk infants.RESULTS:Within the hypothetical NICU, the strategy of ROP examinations identified an average of 45.8 cases of type 1 ROP by discharge, transfer, or 40 weeks’ PMA, and another 1.9 cases were included in the group of infants recommended to have later follow-up. Digital imaging with an ROP examination at discharge identified all 47.7 cases of type 1 ROP. On average, the ROP examination–only strategy required 1745.7 ROP examinations, whereas digital imaging with a discharge examination required 1065.5 ROP examinations and 1786.2 digital imaging sessions.CONCLUSIONS:Although digital imaging decreased the number of ROP examinations per infant, there was an increase in the total number of interventions (ie, ROP examinations and imaging sessions). Providing an ROP examination at the time of NICU discharge can significantly reduce the number of infants who require follow-up.
Apró közlemények
Authors: Bauer Norbert , Balogh Lajos , Bezeczky Árpád , Nagy József , Deák Balázs , Kiss Orsolya , Valkó Orsolya , Schmidt Dávid , Török Péter , Szűcs Péter , Kovács Dániel , Lengyel Attila , Máté András , Somlyay Lajos 
Published: December 2015

1. Az Apium repens (Jacq.) Lagasca új előfordulása a Szigetközben
2. A Limonium gmelinii (Willd.) Kuntze subsp. hungaricum (Klokov) Soó alkalmi megjelenései útpadkákon
3. Az Asparagus verticillatus L. elvadulásának első hazai adatáról
4. A Digitalis lanata Ehrh. új előfordulása Kemencén (Börzsöny)
5. Balkáni csillagvirág (Prospero paratheticum Speta) első előfordulási adata a Duna–Tisza-közén
6. Néhány érdekesebb növényfaj megjelenése a Duna 2013. évi nagy árvize után a Szigetköz hullámterében
7. Az adventív ágas falgyom (Parietaria judaica L.) újabb előfordulási adata Debrecenből
8. Kindbergia praelonga (Hedw.) Ochyra Sopron város mohaflórájában
9. Adatok a Plantago coronopus L. hazai elterjedéséhez
10. A csipkés gyöngyvessző (Spiraea crenata L.) egykori kunpeszéri előfordulásáról
11. A Spiraea crenata L. sas-hegyi (Budai-hegység) felfedezésének története
Diagnóstico prenatal de acretismo placentario: hallazgos y utilidad del ultrasonido y la resonancia magnética. Reporte de casos en el Hospital Universitario de la Fundación Santa Fe de Bogotá (Colombia)
Authors: Wilches-Llanos Aleida , Palazuelos-Jiménez Gloria , Trujillo-Calderón Stephanie , Romero-Enciso Javier 
Published: December 2015

<p><strong>Objetivo:</strong> describir y revisar los hallazgos relevantes en imágenes diagnósticas del abordaje prenatal de pacientes con diagnóstico de acretismo placentario.</p><p><strong>Materiales y métodos:</strong> presentamos los casos de tres mujeres que fueron atendidas en un centro hospitalario de alta complejidad, con factores de riesgo para acretismo placentario y evaluación prenatal por ultrasonido (US) y resonancia magnética (RM), cuyo diagnóstico fue corroborado con estudio anatomopatológico. Se describen los aspectos clínicos, los hallazgos por imágenes y su correlación histológica. Se realizó una búsqueda de la literatura a través de PubMed, Lilacs y EBSCO, se incluyeron artículos originales, revisiones de tema y reportes de casos sobre la utilidad y los aspectos más importantes del US y la RM en el diagnóstico prenatal de acretismo placentario.</p><p><strong>Resultados:</strong> se incluyeron 11 artículos originales, 8 de revisión y 1 reporte caso. La placenta previa asociada a lagunas placentarias en ultrasonido y en RM a bandas hipointensas placentarias y el abombamiento del útero son considerados como los principales signos de acretismo. El US asociado a Doppler color tiene una sensibilidad de 97 % y una especificidad del 92 %. La RM puede definir el compromiso uterino y de los órganos vecinos, con una sensibilidad que varía entre el 77 y el 89,6 %, la especificidad es cercana al 92 %.</p><p><strong>Conclusiones:</strong> el abordaje prenatal precoz a través de las imágenes diagnósticas no invasivas brinda información de utilidad a los clínicos del compromiso y la extensión en la evaluación de pacientes con factores de riesgo para acretismo placentario.</p>