bluuebunny/crossref_metadata_2025_split huggingface dataset:
Febrile Infection-Related Epilepsy Syndrome (FIRES) with Multifocal Subcortical Infarcts, A New Imaging Phenotype
Authors: Tan Ai 
Published: July 2018

AbstractFebrile infection-related epilepsy syndrome (FIRES) is a catastrophic epileptic encephalopathy of unknown etiology which occurs predominantly in school-aged children, following a febrile illness. The term FIRES was first proposed in 2010 by van Baalen et al. The etiology of FIRES remains elusive, although most believed that it is likely related to inappropriate activation of the innate immune system. It is often a diagnosis of exclusion as it lacks specific clinical criteria and/or confirmatory tests. Familiarity with the range of imaging phenotypes associated with FIRES is crucial as this will assist timely recognition and institution of appropriate treatment plan. With this in mind, the author would like to present a rare case of FIRES with extensive subcortical infarcts, predominantly in the temporo-occipital lobes. This has never been reported before and may represent a new imaging phenotype of FIRES. A detailed literature review, focusing on the various pattern of imaging phenotypes, in relation to patients' age and clinical outcome, will also be included.
Pediatric Cervical Lymphadenitis
Authors: Jaggi Preeti , Walz Patrick , Hecht Shaina 
Published: July 2018

AbstractEnlargement of the lymph nodes in the head and neck region is a common presenting symptom in the pediatric population as the upper aerodigestive tract is a common source of inoculation of many infectious agents. While infectious processes—both viral and bacterial and both acute and chronic—are the most likely etiology of enlargement of cervical lymph nodes, other potential causes including inflammatory conditions and malignancy should be considered in the evaluation of cervical adenopathy. In this article, the anatomy and physiology as well as pathophysiology of the head and neck lymphatic system will be reviewed as this relates to clinical presentation of cervical lymphadenitis. Also, the myriad causes for cervical adenopathy will be discussed with a comprehensive review of the epidemiology of infectious etiologies. An evidence-based framework for the diagnostic workup and therapeutic interventions available to appropriately manage infectious cervical lymphadenitis will be reviewed, and the complications that can result from failure to adequately diagnose and treat cervical lymphadenitis will be discussed.
Secondary Bone Defect in Neuromuscular Diseases in Childhood: A Longitudinal “Muscle-Bone Unit” Analysis
Authors: Ribstein C. , Courteix D. , Rabiau N. , Bommelaer C. , Bourdeau Y. , Pereira B. , Sarret Catherine 
Published: July 2018

AbstractTo evaluate the potential bone defect in neuromuscular diseases, we conducted a longitudinal study including three groups of patients: 14 Duchenne muscular dystrophies (DMD) and 2 limb-girdle muscular dystrophies (LGMD); 3 Becker muscular dystrophies (BeMD) and 7 spinal muscular atrophies (SMA). Yearly osteodensitometries assessed body composition and bone mineral density (BMD) associated with bone markers and leptin. Along the 7-year study, 107 osteodensitometries showed that bone status evolved to osteopenia in most patients except BeMD. When analyzing the crude values, BMD improved with age in BeMD and SMA but not in DMD/LGMD. The correlation using the Z-scores displayed a decrease in BMD with age in DMD/LGMD for all regions, in SMA at total body less head, whereas BMD increased in BeMD at lumbar spine. As observed in healthy persons, muscular mass and bone tissue were significantly correlated. Glucocorticoids were deleterious on trabecular and cortical bone. Leptin was high in most patients and correlated to fat mass and bone parameters. This study confirms a secondary bone defect in neuromuscular diseases, further confirming the functional relationship between bone and muscle and arguing for regular bone follow-up in patients to prevent fracture risk. Adipose tissue seems to interfere with bone remodeling in neuromuscular diseases.
Identification of Two Novel Mutations in Aminomethyltransferase Gene in Cases of Glycine Encephalopathy
Authors: Lingappa Lokesh , Naushad Shaik , Radha Rama Devi Akella 
Published: July 2018

AbstractIn this study, we report three cases of nonketotic hyperglycinemia (NKHG) diagnosed biochemically and molecularly. Clinical exome analysis in two families revealed two novel mutations in the aminomethyltransferase (AMT) gene, that is, c.14_15insT (p.Ser6LysfsTer22) and c.259–2A > T, both of them adversely affecting the protein. This is the first report of AMT gene mutations in NKHG from India. Prenatal diagnosis in the first family showed an unaffected fetus in the third pregnancy. The role of AMT protein is pivotal for the synthesis of 5,10-methylene tetrahydrofolate, the first metabolite in one-carbon metabolism that regulates DNA synthesis, repair, and methylation.
Nu-prefaced responses in Russian
conversation
Authors: Bolden Galina B. 
Published: July 2018

Abstract
This chapter examines the Russian particle nu,
focusing on its use in responses to polar and question-word
questions. I show that nu prefaces responses that
are, in some way, misaligned vis-à-vis the initiating action. First,
nu may preface
non-type-conforming responses, i.e., responses
that “depart from the constraints embodied in the grammatical form”
of the question (Raymond
2003, 946). Such responses may operate on the terms
of the question, correct its presuppositions, resist the action the
question implements, and problematize its assumption of
answerability. Second, nu may preface responses
that conform to the question’s grammatical constraints and forward
its action agenda, but convey an incongruent epistemic stance by
suggesting that the questioner already knows the solicited
information.
Turn-initial particles in English
Authors: Heritage John 
Published: July 2018

Abstract
This chapter examines the English turn-initial particles
oh and well. It begins with a
consideration of their distinctive usages and functions in three
basic sequential positions (first, second and third), arguing that
both exhibit what Schegloff
(1996) terms ‘positional sensitivity’. The chapter then
considers some larger contrasts between the two particles, including
distinctions between epistemic (oh) and
action-projecting (well) functions, forward-
(well) and backward- (oh)
looking orientations, and their underlying semantic
characteristics.
Making up one’s mind in second position
Authors: Keevallik Leelo 
Published: July 2018

Abstract
This chapter discusses preferred responses that are delayed in their
turn by the initial particle no in Estonian. It
demonstrates that the turn-initial time-space may be employed for a
display of “making up one’s mind”, either weighing matters outside
the conversation or something already discussed in the talk. The
paper argues that besides the dichotomous choice between the
preferred and the dispreferred answer format, there are individual
contingencies to consider in committing to future actions as made
relevant in requests, proposals and suggestions. By marking a
transition from prior resistance to compliance with a
no-preface, the speaker indexes that the
emerging response is carefully considered and therefore socially
cohesive.
Justifying departures from progressivity
Authors: Heinemann Trine , Steensig Jakob 
Published: July 2018

Abstract
This chapter investigates the use of the Danish particle
altså in turn-initial position. Turn-initial
altså can be employed for prefacing a wide
range of actions, including self- and other-initiated repair,
questions, second stories and answers to both yes/no and
wh-questions. We show that across these actions, participants in
interaction produce altså to indicate (1) that the
action they will produce departs from progressivity, (2) that it
will expand on something prior, (3) that the departure is,
therefore, justified, and (4) that it will contribute to
reinstalling the progression of the larger on-going activity. Some
of the actions that altså prefaces can also be
prefaced by phrases that function like ‘you know’ or ‘I mean’, which
seem to do at least some of the work that altså
does, but altså is used more frequently and across
a wider range of actions. In our discussion, we raise the
possibility that the usefulness of altså is due to
the fact that it allows its producer to indicate that no one party
in the interaction was accountable or at fault for the
departure.
Off-target predictions in CRISPR-Cas9 gene editing using deep learning
Authors: Lin Jiecong , Wong Ka-Chun 
Published: July 2018

Abstract

Motivation
The prediction of off-target mutations in CRISPR-Cas9 is a hot topic due to its relevance to gene editing research. Existing prediction methods have been developed; however, most of them just calculated scores based on mismatches to the guide sequence in CRISPR-Cas9. Therefore, the existing prediction methods are unable to scale and improve their performance with the rapid expansion of experimental data in CRISPR-Cas9. Moreover, the existing methods still cannot satisfy enough precision in off-target predictions for gene editing at the clinical level.

Results
To address it, we design and implement two algorithms using deep neural networks to predict off-target mutations in CRISPR-Cas9 gene editing (i.e. deep convolutional neural network and deep feedforward neural network). The models were trained and tested on the recently released off-target dataset, CRISPOR dataset, for performance benchmark. Another off-target dataset identified by GUIDE-seq was adopted for additional evaluation. We demonstrate that convolutional neural network achieves the best performance on CRISPOR dataset, yielding an average classification area under the ROC curve (AUC) of 97.2% under stratified 5-fold cross-validation. Interestingly, the deep feedforward neural network can also be competitive at the average AUC of 97.0% under the same setting. We compare the two deep neural network models with the state-of-the-art off-target prediction methods (i.e. CFD, MIT, CROP-IT, and CCTop) and three traditional machine learning models (i.e. random forest, gradient boosting trees, and logistic regression) on both datasets in terms of AUC values, demonstrating the competitive edges of the proposed algorithms. Additional analyses are conducted to investigate the underlying reasons from different perspectives.

Availability and implementation
The example code are available at https://github.com/MichaelLinn/off_target_prediction. The related datasets are available at https://github.com/MichaelLinn/off_target_prediction/tree/master/data.
Biblical Hebrew Bal and Privative Negation
Authors: Sjörs Ambjörn 
Published: July 2018

Abstract
The Biblical Hebrew lexeme bal has been described as a poetic and prophetic synonym with lō’ in previous research. However, cognate morphemes in the Semitic languages outside Northwest Semitic, as well as other Biblical Hebrew lexemes derived from the relevant root morpheme, e.g. bǝlî and lǝḇiltî, may be identified with privative grammatical morphemes, i.e. grammatical morphemes that cancel an association. It is argued that, most of the time, bal too should be identified with privative negation, and that it is a poetic and prophetic synonym with lǝḇiltî (with different co-occurrence restrictions). Other times, the uses of bal can be explained as typical for the grammaticalization of privative expressions. The use of bal as a negator, for example, can be explained in terms of the grammaticalization of a conventional implicature, by which a salient feature, privation, became bleached semantically in favour of its implicature, negation.1
Intergenerational effects on mouse sperm quality after in utero exposure to acetaminophen and ibuprofen
Authors: Rossitto Moïra , Marchive Candice , Pruvost Alain , Sellem Eli , Ghettas Aurélie , Badiou Stéphanie , Sutra Thibault , Poulat Francis , Philibert Pascal , Boizet-Bonhoure Brigitte 
Published: July 2018

ABSTRACTNonsteroidal antiinflammatory drugs and analgesic drugs, such as N‐acetyl‐p‐aminophenol (APAP; acetaminophen, paracetamol), are widely used by pregnant women. Accumulating evidence has indicated that these molecules can favor genital malformations in newborn boys and reproductive disorders in adults. However, the consequences on postnatal testis development and adult reproductive health after exposure during early embryo‐genesis are still unknown. Using the mouse model, we show that in utero exposure to therapeutic doses of the widely used APAP‐ibuprofen combination during the sex determination period leads to early differentiation and decreased proliferation of male embryonic germ cells, and early 5‐mefhylcytosine and extracellular matrix protein deposition in 13.5 d postcoitum exposed testes. Consequently, in postnatal testes, Sertoli‐cell maturation is delayed, the Leydig‐cell compartment is hyperplasia and the spermatogonia A pool is decreased. This results in a reduced production of testosterone and in epididymal sperm parameter defects. We observed a reduced sperm count (19%) in utero–exposed (FO) adult males and also a reduced sperm motility (40%) in their offspring (Fl) when both parents were exposed, which leads to subfertility among the 6 mo old Fl animals. Our study suggests that the use of these drugs during the critical period of sex determination affects the germ‐line development and leads to adverse effects that could be passed to the offspring.—Rossitto, M., Marchive, C., Pruvost, A., Sellem, E., Ghettas, A., Badiou, S., Sutra, T., Poulat, F., Philibert, P., Boizet‐Bonhoure, B. Intergenerational effects on mouse sperm quality after in utero exposure to acetaminophen and ibuprofen. FASEB J. 33, 339–357 (2019). www.fasebj.org
Charting Tissue Expression Anatomy by Spatial Transcriptome Decomposition
Authors: Maaskola Jonas , Bergenstråhle Ludvig , Jurek Aleksandra , Navarro José Fernández , Lagergren Jens , Lundeberg Joakim 
Published: July 2018

We create data-driven maps of transcriptomic anatomy with a probabilistic framework for unsupervised pattern discovery in spatial gene expression data. With convolved negative binomial regression we discover patterns which correspond to cell types, microenvironments, or tissue components, and that consist of gene expression profiles and spatial activity maps. Expression profiles quantify how strongly each gene is expressed in a given pattern, and spatial activity maps reflect where in space each pattern is active. Arbitrary covariates and prior hierarchies are supported to leverage complex experimental designs.We demonstrate the method with Spatial Transcriptomics data of mouse brain and olfactory bulb. The discovered transcriptomic patterns correspond to neuroanatomically distinct cell layers. Moreover, batch effects are successfully addressed, leading to consistent pattern inference for multi-sample analyses. On this basis, we identify known and uncharacterized genes that are spatially differentially expressed in the hippocampal field between Ammon’s horn and the dentate gyrus.
A Framework for Predicting Design Failures in Engineered Genetic Codes
Authors: Yu Bea , Murphy Matthew , Carr Peter A. 
Published: July 2018

AbstractExtreme engineering of an organism’s genetic code could impart true genetic incompatibility, even blocking effects of horizontal gene transfer and viral infection. Recent experiments exploring this possibility demonstrate that such radical genome engineering achievements are plausible. However, it is unclear when the modifications will compromise the fitness of an organism. Efforts to reformat an entire genome are difficult and expensive; computational methods predicting fruitful experimental trajectories could play a pivotal role in advancing such efforts. We present a framework for building in silico models to assist genome-scale engineering. Genetic code engineering requires choosing from many possible codon-usage schemes, to find a design that is viable and effective. We use machine learning to identify which alternative codon-usage schemes are likely to result in no observed viable cells. Our data-driven approach employs observations of how modifying codon usage in individual genes impacted observed viability in E. coli, revealing salient features for early identification of problematic genetic code designs. We achieved an average area under the receiver operating characteristic of 0.72 on out-ofsample data.Author SummaryAs machine learning and artificial intelligence play an increasingly central role in science and engineering, it will be important to establish standardized techniques that facilitate the dialogue between experimentation and modeling. Biological experimental techniques are concurrently evolving at a rapid pace, providing unique opportunities to collect high-quality, novel information that was previously unobtainable. This work navigates the landscape of this vast, new territory, identifies interesting landmarks for exploration and posits new approaches towards advancing our research efforts in these areas. In this work, we show that, using a small dataset of 47 observations and rigorous nested cross validation techniques, we can build a model that makes better-than-random predictions of how codon usage changes in essential genes influence viability in E. coli. These predictions can be used to inform experimental trajectories in both genetic code and codon optimization experiments. We discuss ways to improve this model, iteratively, by performing high value experiments that decrease uncertainty in predictions and extrapolation error. Finally, we present novel visualization methods to aid in developing intuitions for how re-coding impacts groups of genes. These methods are also useful tools in building important insights into how well machine learning algorithms can generalize to new data.
Leucine rich repeat kinase 2 (LRRK2) gly2019ser mutation is absent in a second cohort of nigerian africans with parkinson disease
Authors: Okubadejo Njideka U , Rizig Mie , Ojo Oluwadamilola O , Jonvik Hallgeir , Oshinaike Olajumoke , Brown Emmeline , Houlden Henry 
Published: July 2018

ABSTRACTTo date the LRRK2 p.G2019S mutation remains the most common genetic cause of Parkinson disease (PD) worldwide. It accounts for up to 6% of familial and approximately 1.5% of sporadic cases. LRRK2 has a kinase enzymatic domain which provides an attractive potential target for drug therapies and LRRK2 kinase inhibitors are in development. Prevalence of the p.G2019S has a variable ethnic and geographic distribution, the highest was reported among Ashkenazi Jews (30% in patients with familial PD, 14% in sporadic PD, 2.0% in controls) and North African Berbers (37% in patients with familial PD, 41% in sporadic PD, and 1% in controls). Little is known about the frequency of the LRRK2 p.G2019S among populations in Sub Saharan Africa. Our group and others previously reported that the p.G2019S is absent in a small cohort from Nigerian PD patients and controls. Here we used Kompetitive Allele Specific PCR (KASP) assay to screen for the p.G2019S in a larger cohort of Black African PD patients (n =126) and healthy controls (n = 55) from Nigeria. Our analysis confirmed that all patients and controls are negative for the p.G2019S mutation. This report provides further evidence that the LRRK2 p.G2019S is not implicated in PD in black populations from Nigeria and support the notion that p.G2019S mutation originated after the early human dispersal from sub-Saharan Africa. Further studies using larger cohorts and advance sequencing technology are required to underpin the genetic causes of PD in this region.
Employee indifference and inaction against abusive supervision
Authors: Zhang Yucheng , Frenkel Stephen J. 
Published: July 2018

PurposeThe purpose of this paper is to investigate how part-time waiters perceive and respond to abusive supervision by the owner-manager of a small restaurant.Design/methodology/approachAn ethnographic approach was used to collect data. One of the authors worked as a participant observer for three months. In addition, 13 interviews and three focus group discussions were conducted.FindingsData analysis showed how neutral identification based on a primary identity—liu xu sheng(overseas student)—overshadows employees’ occupational identity (waiter), which helps waiters to cope with abusive supervision.Originality/valueDevelopment and application of the concept of neutral organizational identification orientation encourages emotional suppression and reframing, leading to waiters’ indifference and acquiescence in abusive supervision. Implications are drawn for theory and the practice of managing part-time and temporary workers.
Numerical simulation of two-phase flow regime in horizontal pipeline and its validation
Authors: Ban Sam , Pao William , Nasif Mohammad Shakir 
Published: July 2018

Purpose
The purpose of this paper is to investigate oil-gas slug formation in horizontal straight pipe and its associated pressure gradient, slug liquid holdup and slug frequency.

Design/methodology/approach
The abrupt change in gas/liquid velocities, which causes transition of flow patterns, was analyzed using incompressible volume of fluid method to capture the dynamic gas-liquid interface. The validity of present model and its methodology was validated using Baker’s flow regime chart for 3.15 inches diameter horizontal pipe and with existing experimental data to ensure its correctness.

Findings
The present paper proposes simplified correlations for liquid holdup and slug frequency by comparison with numerous existing models. The paper also identified correlations that can be used in operational oil and gas industry and several outlier models that may not be applicable.

Research limitations/implications
The correlation may be limited to the range of material properties used in this paper.

Practical implications
Numerically derived liquid holdup and holdup frequency agreed reasonably with the experimentally derived correlations.

Social implications
The models could be used to design pipeline and piping systems for oil and gas production.

Originality/value
The paper simulated all the seven flow regimes with superior results compared to existing methodology. New correlations derived numerically are compared to published experimental correlations to understand the difference between models.