bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pragmatics in task-based language assessment
Authors: Timpe-Laughlin Veronika 
Published: July 2018

Abstract
Several researchers have pointed out synergies between task-based language assessment (TBLA) and L2 pragmatics assessment, insofar as both domains are based on a concern for effective communication in context (Kim & Taguchi, 2015; Norris, 2016; Timpe-Laughlin, Wain, & Schmidgall, 2015). It is therefore surprising that very little research has been carried out on pragmatics in TBLA. Kim and Taguchi (2015), for example, highlighted that “[p]ragmatics has been a particularly underinvestigated area of task-based research” (p. 660), both in teaching and assessment – a paradox given that the task-based assessment paradigm provides a fitting framework for the assessment of L2 pragmatics. Bringing together the two lines of research – L2 pragmatics and TBLA – this chapter will highlight similarities between the basic tenets of both domains, while discussing opportunities and challenges for employing TBLA as a framework for designing assessments that measure L2 pragmatics. To that end, the chapter begins with a brief review of the fundamental concepts of task-based assessment, highlighting the role of the task as a basic unit of analysis in designing tests that include a focus on pragmatics. It discusses challenges related to generalizability, reliability, and validity as well as issues of task design and task difficulty. It then canvasses current uses of TBLA to assess L2 pragmatics, illustrating different types of task-based assessments that have included pragmatic phenomena, both in research and in operational testing. Ultimately, it argues that, as a foundation for assessing L2 pragmatics, tasks offer a number of benefits that, despite the challenges, are worth pursuing.
ACDtool: a web-server for the generic analysis of large data sets of counts
Authors: Claverie Jean-Michel , Ta Thi Ngan 
Published: July 2018

Abstract

Motivation
More than 20 years ago, our laboratory published an original statistical test [referred to as the Audic-Claverie (AC) test in the literature] to identify differentially expressed genes from the pairwise comparison of counts of ‘expressed sequence tags’ determined in different conditions. Despite its antiquity and the publications of more sophisticated packages, this original publication continued to gather more than 200 citations per year, indicating the persistent usefulness of the simple AC test for the community. This prompted us to propose a fully revamped version of the AC test with a user interface adapted to the diverse and much larger datasets produced by contemporary omics techniques.

Results
ACDtool is a freely accessible web-service proposing three types of analyses: (i) the pairwise comparison of individual counts, (ii) pairwise comparisons of arbitrary large lists of counts and (iii) the all-at-once pairwise comparisons of multiple datasets. Statistical computations are implemented using standard R functions and can accommodate all practical ranges of counts as generated by modern omic experiments. ACDtool is well suited for large datasets without replicates.

Availability and implementation
http://www.igs.cnrs-mrs.fr/acdtool/

Supplementary information
Supplementary data are available at Bioinformatics online.
Effects on the bycatch of eulachon and juvenile groundfish by altering the level of artificial illumination along an ocean shrimp trawl fishing line
Authors: Lomeli Mark J M , Groth Scott D , Blume Matthew T O , Herrmann Bent , Wakefield W Waldo 
Published: July 2018

Abstract
We examined how catches of ocean shrimp (Pandalus jordani), eulachon (Thaleichthys pacificus), and juvenile groundfish could be affected by altering the level of artificial illumination along the fishing line of an ocean shrimp trawl. In the ocean shrimp trawl fishery, catches of eulachon are of special concern, as the species’ southern Distinct Population Segment is listed as “threatened” under the US Endangered Species Act. Using a double-rigged trawl vessel, with one trawl illuminated and the other unilluminated, we compared the catch efficiencies for ocean shrimp, eulachon, and juvenile groundfish between an unilluminated trawl and trawls illuminated with 5, 10, and 20 LED fishing lights along their fishing line. The addition of artificial illumination along the trawl fishing line significantly affected the average catch efficiency for eulachon, rockfish (Sebastes spp.), and flatfish, with the three LED configurations each catching significantly fewer individuals than the unilluminated trawl without impacting ocean shrimp catches. For Pacific hake (Merluccius productus), the ten LED-configured trawl caught significantly more fish than the unilluminated trawl. For the five and 20 LED configurations, mean Pacific hake catches did not differ from the unilluminated trawl. This study contributes new data on how artificial illumination can affect eulachon catches (and other fish) and contribute to their conservation.
A Case of Lassa Fever Diagnosed at a Community Hospital—Minnesota 2014
Authors: Choi Mary J , Worku Shewangizaw , Knust Barbara , Vang Arnold , Lynfield Ruth , Mount Mark R , Objio Tina , Brown Shelley , Griffith Jayne , Hulbert Deborah , Lippold Susan , Ervin Elizabeth , Ströher Ute , Holzbauer Stacy , Slattery Wendolyn , Washburn Faith , Harper Jane , Koeck Mackenzie , Uher Carol , Rollin Pierre , Nichol Stuart , Else Ryan , DeVries Aaron 
Published: July 2018

Abstract

Background
In April 2014, a 46-year-old returning traveler from Liberia was transported by emergency medical services to a community hospital in Minnesota with fever and altered mental status. Twenty-four hours later, he developed gingival bleeding. Blood samples tested positive for Lassa fever RNA by reverse transcriptase polymerase chain reaction.

Methods
Blood and urine samples were obtained from the patient and tested for evidence of Lassa fever virus infection. Hospital infection control personnel and health department personnel reviewed infection control practices with health care personnel. In addition to standard precautions, infection control measures were upgraded to include contact, droplet, and airborne precautions. State and federal public health officials conducted contract tracing activities among family contacts, health care personnel, and fellow airline travelers.

Results
The patient was discharged from the hospital after 14 days. However, his recovery was complicated by the development of near complete bilateral sensorineural hearing loss. Lassa virus RNA continued to be detected in his urine for several weeks after hospital discharge. State and federal public health authorities identified and monitored individuals who had contact with the patient while he was ill. No secondary cases of Lassa fever were identified among 75 contacts.

Conclusions
Given the nonspecific presentation of viral hemorrhagic fevers, isolation of ill travelers and consistent implementation of basic infection control measures are key to preventing secondary transmission. When consistently applied, these measures can prevent secondary transmission even if travel history information is not obtained, not immediately available, or the diagnosis of a viral hemorrhagic fever is delayed.
Infectious Complications of Multiple Sclerosis Therapies: Implications for Screening, Prophylaxis, and Management
Authors: Epstein David J , Dunn Jeffrey , Deresinski Stan 
Published: July 2018

Abstract
Multiple sclerosis therapies include interferons, glatiramer, and multiple immunosuppressive drugs. Discerning infectious risks of immunosuppressive drugs requires understanding their mechanisms of action and analyzing interventional studies and postmarketing observational data. Though identical immunosuppressive therapies are sometimes used in non-neurologic conditions, infectious risks may differ in this population. Screening for and treatment of latent tuberculosis (TB) infection should be prioritized for patients receiving alemtuzumab; ocrelizumab is likely not associated with an increased risk of TB. Hepatitis B virus (HBV) reactivation can be devastating for patients treated with ocrelizumab and alemtuzumab, whereas the small molecule oral agents do not likely pose substantial risk of HBV. Progressive multifocal leukoencephalopathy is a particular concern with natalizumab. Alemtuzumab, and possibly natalizumab and fingolimod, risks herpes virus reactivation and may warrant prophylaxis. Unusual opportunistic infections have been described. Vaccination is an important tool in preventing infections, though vaccine timing and contraindications can be complex.
Chemosensory bitter taste receptors (T2Rs) are activated by multiple antibiotics
Authors: Jaggupilli Appalaraju , Singh Nisha , De Jesus Vivianne Cruz , Gounni Mohamed Soussi , Dhanaraj Premnath , Chelikani Prashen 
Published: July 2018

ABSTRACTMany medications including antibiotics taste bitter. The potency of these antibiotics on the 25 bitter taste receptors (T2Rs) in humans remains poorly understood. Here we characterize by sensory and structure‐function analyses how antibiotics frequently used to treat airway infections in cystic fibrosis activate multiple human T2Rs. The potency of the broad‐spectrum antibiotics, tobramycin, levofloxacin, and azithromycin on the highly expressed T2Rs in airways, T2R4, T2R14, and T2R20 was pursued. The amino acids and structural features of T2R4, T2R14, and T2R20 important for antibiotic binding were characterized by mutational analysis in heterologous cell‐based assays. Strikingly, extracellular loop 2 in T2Rs performs a key function in binding to antibiotics with contribution from residues in transmembrane helices. Our results suggest that different antibiotics activate multiple T2Rs with different potencies. An understanding of the nonantibiotic and physiologic effects mediated through T2Rs on the host cells is much needed.—Jaggupilli, A., Singh, N., De Jesus, V. C., Gounni, M. S., Dhanaraj, P., Chelikani, P. Chemosensory bitter taste receptors (T2Rs) are activated by multiple antibiotics. FASEB J. 33, 501–517 (2019). www.fasebj.org
Precision medicine in food allergy
Authors: Arasi Stefania , Mennini Maurizio , Valluzzi Rocco , Riccardi Carla , Fiocchi Alessandro 
Published: July 2018

Purpose of review
To familiarize the reader with the concept of precision medicine in food allergy through the most recent insights in the diagnosis, prognosis, and management of the disease.

Recent findings
With the advent of omics sciences, a new era is commencing. Food protein allergens characterization and quantification together with the immunoglobulin E epitope mapping will contribute to the diagnosis/prognosis of food allergy and will lead to a better safety assessment of foods. The characterization of biomarkers able to identify specific phenotypes and endotypes will improve the diagnostic accuracy. This together with a better understanding of mechanisms of action of the different therapeutic options will allow the accurate selection of the appropriate patient.

Summary
In the near future, advances in technologies and data interpretation will allow a better understanding of the pathogenesis of food allergy and the development of a personalized treatment tailored on the specific patient’ profile.
Maternal Protective Parenting Accounts for the Relationship Between Pain Behaviors and Functional Disability in Adolescents
Authors: Lynch-Jordan Anne M. , Peugh James , Cunningham Natoshia R. , Trygier Jessica R. , Kashikar-Zuck Susmita 
Published: July 2018

Introduction:
A variety of factors influence parent responses to pain behaviors they observe in their adolescents with chronic pain. Certain parental responses to pain, such as attention or overprotection, can adversely impact adolescent adaptive functioning and correspond to poor clinical outcomes.

Objectives:
It was hypothesized that the relationship between adolescent pain behaviors and functional disability was mediated by maladaptive parenting (protective, monitoring, solicitousness) responses.

Materials and Methods:
Participants were 303 adolescents and their mothers presenting to a pain clinic. Adolescents completed measures of functional disability and pain intensity; mothers completed measures assessing adolescent pain behaviors, their own catastrophizing about their adolescent’s pain, and responses to pain. A path model tested the direct and indirect associations between pain behaviors and disability via 3 parenting responses, controlling for average pain intensity and parent pain catastrophizing.

Results:
Greater pain behavior was associated with increased protective responses (α path, P<0.001); greater protective behavior was associated with increased disability (β path, P=0.002). Including parenting responses in the model, the path between pain behaviors and disability remained significant (c′ path, P<0.001). The indirect path between pain behaviors and disability via parenting responses was significant for protective responses (P<0.02), controlling for pain intensity and parent pain catastrophizing. The indirect effect of protective responses explained 18% of the variance between pain behaviors and disability.

Discussion:
Observing adolescent pain behaviors may prompt parents to engage in increased protective behavior that negatively impacts adolescents’ functioning, even after controlling for the effects of parental pain catastrophizing.
Opioid Dependence and Health Care Utilization After Decompression and Fusion in Patients With Adult Degenerative Scoliosis
Authors: Sharma Mayur , Ugiliweneza Beatrice , Sirdeshpande Pooja , Wang Dengzhi , Boakye Maxwell 
Published: July 2018

Study Design.
Retrospective study.

Objective.
To identify factors associated with opioid dependence after surgery for adult degenerative scoliosis (ADSc).

Summary of Background Data.
Opioid epidemic is of prodigious concern throughout the United States.

Methods.
Data was extracted using national MarketScan database (2000–2016). Opioid dependence was defined as continued opioid use or >10 opioid prescriptions for 1 year either before or 3 to 15 months after the procedure. Patients were segregated into four groups based on opioid dependence before and postsurgery: NDND (before nondependent who remain non-dependent), NDD (before nondependent who become dependent), DND (before dependent who become non-dependent) and DD (before dependent who remain dependent). Outcomes were discharge disposition, length of stay, complications, and healthcare resource utilization.

Results.
Approximately, 35.82% (n = 268) of patients were identified to have opioid dependence before surgery and 28.34% (n = 212) were identified to have opioid dependence after surgery for ADSc. After surgical fusion for ADSc, patients were twice likely to become opioid independent than they were to become dependent (13.77% vs. 6.28%, OR: 2.191, 95% CI: 21.552–3.094; P < 0.0001). Before opioid dependence (RR: 14.841; 95% CI: 9.867, 22.323; P < 0.0001) was identified as a significant predictor of opioid dependence after surgery for ADSc. In our study, 57.9%, 6.28%, 13.77%, and 22.06% of patients were in groups NDND, NDD, DND, and DD respectively. DD and NDD were likely to incur 3.03 and 2.28 times respectively the overall costs compared with patients’ ingroup NDND (P < 0.0001), at 3 to 15 months postsurgery (median $21648 for NDD; $40,975 for DD; and $ 13571 for NDND groups).

Conclusion.
Surgery for ADSc was not associated with increased likelihood of opioid dependence, especially in opioid naïve patients. Patients on regular opiate treatment before surgery were likely to remain on opiates after surgery. Patients who continued to be opioid dependent or become dependent after surgery incur significantly higher healthcare utilization at 3 and 3 to 15 months.

Level of Evidence: 4
Tissue Contraction—A New Paradigm in Breast Reconstruction
Authors: Becker Hilton , Zhadan Olga 
Published: July 2018

Background:
Skin expansion is commonly needed in order to reconstruct the breast following modified radical mastectomy. With the advent of skin-sparing and nipple-sparing techniques, expansion is no longer necessary. The natural ability of healing tissues to contract can be advantageously used to improve the outcomes of immediate prepectoral breast reconstruction.

Methods:
A prospective analysis of the results of 20 prepectoral breast reconstructions following skin-sparing or nipple-sparing mastectomies was performed. Reconstruction was performed using the adjustable breast implant initially underfilled with air. No acellular dermal matrix or mesh support was used. Further air was added during the follow-up office visits. Air was replaced with normal saline when the desired breast size was achieved. The adjustable implants were replaced with silicone gel implants when necessary.

Results:
Contraction of the skin flap over the underfilled implant was noticed in all patients. Five patients (25%) developed a seroma, and 2 patients had hematoma of the breast pocket. Wound-edge necrosis required debridement in 2 patients (10%). Complications were all resolved without implant loss.

Conclusions:
Tissue contraction can be successfully utilized in breast reconstruction following skin-sparing and nipple-sparing mastectomy. Contraction results in thickening and elevation of the flap, eliminating the need for skin excision or the use of acellular dermal matrix. The partially filled implant functions as a spacer, preventing the flap from adhering to the underlying muscle and avoiding pressure on the skin flap.
SENSITIVITY OF 840-nm SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY IN DETECTING TYPE 1 NEOVASCULARIZATION ACCORDING TO THE HEIGHT OF THE ASSOCIATED PIGMENT EPITHELIAL DETACHMENT
Authors: Mrejen Sarah , Giocanti-Auregan Audrey , Tabary Sandrine , Cohen Salomon Y. 
Published: July 2018

Purpose:
To evaluate the ability of optical coherence tomography angiography (OCTA) to detect abnormal vascular blood flow in Type 1 neovascularization (NV) with or without significant pigment epithelial detachment (PED).

Methods:
Consecutive age-related macular degeneration patients with either treatment-naive or anti–vascular endothelial growth factor–treated Type 1 NV were divided into 2 groups based on the PED height on structural OCT: greater than 250 μm (Group 1) versus less than 250 μm (Group 2). Two independent senior retina specialists analyzed the OCTA images (Zeiss Angioplex OCT, Carl Zeiss AG, Jena, Germany) using the automatic slabs alone (first reader) versus automatic and manual segmentation slabs (second reader).

Results:
In Group 1, 15 men and 42 women, aged from 51 years to 97 years (mean: 87.5), were included. Optical coherence tomography angiography was able to show an abnormal blood flow suggestive of Type 1 NV in 23 (40.3%) of 57 eyes for the first reader and in 32 (56.1%) of 57 eyes for the second reader. In Group 2, 7 men and 30 women, aged from 60 years to 96 years (mean: 80.2), were included. The first and second readers were able to observe an image suggestive of Type 1 NV in 33/37 (89.2%) and 37/37 (100%) of eyes, respectively.

Conclusion:
The ability of OCTA to detect an abnormal blood flow in Type 1 NV was found to highly depend on the height of the associated PED and the use of manual segmentation slabs. Our results suggest that automatic slabs of OCTA should be interpreted with caution for the diagnosis of vascularized PED. The diagnosis of Type 1 NV using OCTA requires the use of manual segmentation and a multimodal imaging approach, especially when the height of the associated PED is >250 μm.
VISUAL FUNCTION AND RETINAL CHANGES IN PATIENTS WITH BIPOLAR DISORDER
Authors: Garcia-Martin Elena , Gavin Alicia , Garcia-Campayo Javier , Vilades Elisa , Orduna Elvira , Polo Vicente , Larrosa Jose M. , Pablo Luis E. , Satue Maria 
Published: July 2018

Purpose:
To evaluate visual and retinal changes in patients with bipolar disorder. To analyze the correlation between structural changes and visual function parameters.

Methods:
Thirty patients with bipolar disorder and 80 healthy controls underwent visual function evaluation with Early Treatment Diabetic Retinopathy Study charts at 100%, 2.50%, and 1.25% contrast, Pelli-Robson chart, and color vision Farnsworth and Lanthony tests. Analysis of the different retinal layers was performed using Spectralis optical coherence tomography with automated segmentation software. Correlation analysis between structural and functional parameters was conducted.

Results:
Patients with bipolar disorder presented worse color vision compared with controls (Lanthony's index, P = 0.002). Full macular thickness, the retinal nerve fiber layer (RNFL), ganglion cell layer, and inner plexiform layer were reduced in patients compared with healthy individuals (P < 0.005). The inner nuclear layer was significantly thickened in patients (P < 0.005). Peripapillary RNFL thickness was reduced in all temporal sectors (P < 0.005). Significant correlations were found between visual acuity and the RNFL thickness, the Pelli-Robson score and the inner plexiform layer, and between the Lanthony's color index and the ganglion cell layer thickness.

Conclusion:
Patients with bipolar disorder present quantifiable thinning of the macular RNFL, ganglion cell layer, and inner plexiform layer, as well as in the peripapillary RNFL thickness, and increasing thinning in the inner nuclear layer.
CONGENITAL TOXOPLASMOSIS ASSOCIATED WITH TRACTIONAL RETINAL DETACHMENT
Authors: Rassi Alessandra , Todorich Bozho , Faia Lisa J. , Trese Michael , Drenser Kimberly , Capone Antonio 
Published: July 2018

Purpose:
We report a case of congenital toxoplasmosis associated with retinal detachment.

Methods:
A 9-month-old white boy presented a unilateral tractional retina detachment associated with congenital toxoplasmosis retinochoroiditis.

Results:
The diagnosis is supported by positive IgG (>400) for toxoplasmosis and intracranial calcification on magnetic resonance imaging, along with positive family history of Toxoplasma infection in the mother.

Conclusion:
Tractional retinal detachment is an infrequent and unconventional presentation of congenital Toxoplasma infection. Inflammatory interference with normal sequence of vitreous development may explain pathogenesis of tractional retinal detachments in the setting of congenital ocular toxoplasmosis.