bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Treatment Motivation Levels on Patients Sent to a Conditional Substance Abuse Treatment Program
Authors: Bulut Sefa , Bozkurt İlhan
Published: February 2019

The main purpose of this study is to examine the effect of treatment motivation levels on substance abuse behaviors of patients sent to a substance dependence treatment program based on the decision of Supervised Release made during a six-week psycho-educational group treatment program. The sample consisted of 112 participants who applied to the Ministry of Health Turkey, Sakarya University Training and Research Hospital, Psychiatry Clinic between the years 2012–2014, and were selected among patients who attended a six-week treatment program. The Treatment Motivation Questionnaire (TMQ), Demographic Information Questionnaire and interview methods were used in data collection. Patients with high treatment motivation levels were found to have a low substance abuse rate, and their adaptation to the treatment program was high. Patients who had high motivation levels at the beginning of the treatment, had low rates of substance abuse at the end of the treatment. This trend was confirmed for all of the measured four sub-types of motivation.
Modulación de las respuestas fisiológicas ante estímulos afectivos: una herramienta para investigar procesos psicológicos
Authors: Gantiva Carlos , Casas María , Ballén Yeraldín , Sotaquirá Miguel , Romo-González Tania
Published: February 2019

El estudio de los procesos psicológicos suele realizarse a partir de medidas de autorreporte y, en algunos casos, a través de tareas conductuales. Sin embargo, cada vez es más necesario obtener medidas más precisas y objetivas de las respuestas psicológicas para fortalecer las conclusiones de los estudios y su alcance. Por lo anterior, el objetivo del presente estudio fue analizar los cambios en distintas respuestas fisiológicas ante estímulos con diferente contenido afectivo, para obtener indicadores fisiológicos de los procesos atencionales, emocionales y motivacionales. Se registraron las respuestas de 40 participantes mientras observaban estímulos apetitivos, neutrales y aversivos. Los resultados muestran que los estímulos apetitivos y aversivos generan mayor respuesta de conductividad de la piel, lo que indica mayor activación simpática y mayor respuesta de orientación, así como mayor desaceleración de la tasa cardiaca y mayor inhibición prepulso, lo que sugiere una mayor respuesta atencional. También se encontró que los estímulos aversivos potencian el reflejo de sobresalto y los apetitivos lo inhiben, lo que lo convierte en un marcador fisiológico de la respuesta motivacional. No se encontraron diferencias significativas entre hombres y mujeres. En conjunto, los resultados apoyan el uso de estas metodologías para el estudio de la orientación/atención, la emoción y la motivación.
Description and observations on morphology and biology of Imparipes clementis sp. nov., a new termite associated scutacarid mite species (Acari, Heterostigmatina: Scutacaridae; Insecta, Isoptera: Rhinotermitidae)
Authors: Baumann Julia , Ferragut Francisco
Published: February 2019

A new species of Scutacaridae (Acari: Heterostigmatina: Pygmephoroidea) associated with Reticulitermes banyulensis Clément, 1978 termites (Isoptera: Rhinotermitidae) is described from Spain. By rearing the mites in laboratory cultures, all life stages (larva, female and male) of Imparipes clementis Baumann sp. nov. were available for descriptions, and information on the mites’ biology could be provided. As the new species strongly resembles I. adleri Delfinado & Baker, 1976, a multivariate morphometric analysis was performed to further support its species status.
Predicting radiation-induced carbon contamination of EUV optics
Authors: Hollenshead Jeromy T. , Klebanoff Leonard E. , Delgado Gil
Published: February 2019

Predictions are made for the radiation-induced carbon contamination threat to ruthenium-coated extreme ultraviolet (EUV) optics for a range of incident EUV intensities, exposure pressures and types of hydrocarbon. A calculational philosophy is developed that acknowledges the ruthenium capping layer may have adsorbed oxygen on it and that the carbon contamination film is partially hydrogenated. The calculations incorporate the Nitta Multisite Adsorption framework, which accounts for the configurational adsorption difficulty encountered by the adsorption of large molecules on surfaces. Contributions from “out-of-band” radiation are included, both in the direct photon-induced dissociation of hydrocarbon molecules and in the out-of-band production of secondary electrons. For the hydrocarbon molecules, n-tetradecane, n-dodecane, n-decane, and benzene, for a range of EUV powers and hydrocarbon pressures, predictions are made for carbon thicknesses, the overall carbon deposition rates, and the relative amounts of contamination produced by primary photon excitation, secondary electrons, and out-of-band radiation. The comparison is made to relevant prior experiments. The model, with no adjustable parameters, provides a good account of prior experiments on n-tetradecane, n-decane, and benzene over the pressure ranges examined by the experiments (∼1 × 10−10 to ∼1 × 10−7 Torr) and over the EUV intensity range 0.001–100 mW/mm2. The level of agreement is within a factor of ∼4 or better, which is consistent with expectations based on the experimental uncertainties. Comparison with prior data for n-decane indicates that the carbon deposit produced by the EUV-induced dissociation of hydrocarbons is substantially hydrogenated. Out-of-band radiation accounts for ∼9%–12% of the overall optic contamination. Secondary electrons account for ∼2% of the overall optic contamination. The results show that the dominant mechanistic cause of the EUV carbon contamination is primary photon absorption by the adsorbed hydrocarbon molecule. The removal of carbon or hydrogen by electron stimulated desorption due to secondary electrons or photon stimulated desorption by primary EUV absorption can be safely ignored as negligible compared to the EUV-induced carbon deposition rate. The results allow comparison with past experiments, provide a framework for conducting future experiments, and predict contamination threats relevant for practical EUV lithography tool operation. The calculations also clarify the underlying physical phenomena at work in the EUV carbon contamination problem.
Electrical and optical properties of wide-gap n-type Sn2Ta2O7 films
Authors: Suzuki Shunichi , Nishio Keishi , Kikuchi Naoto
Published: February 2019

Wide-gap n-type Sn2Ta2O7 polycrystalline films were prepared by RF-magnetron sputtering followed by annealing in a reducing atmosphere (N2). Sn2Ta2O7 is known to show both p- and n-type conductivity. The electrical and optical properties of the films were examined as a function of annealing time. The bandgap of the film was estimated to be 2.7 or 3.2 eV assuming an indirect or direct transition, respectively. The electrical conductivity of the film at 300 K increased from 2.1 × 10−8 S cm−1 (as-deposited) to a maximum of 2.1 S cm−1 (annealed for 14 h). The temperature dependence of the conductivity changed from semiconducting to degenerate semiconducting behavior with increasing annealing time, suggesting that oxygen vacancies were generated by the annealing in N2. From the temperature dependence of the mobility, it was found that neutral impurities were the dominant scattering centers for electron carriers.
Chronic TGF-β exposure drives stabilized EMT, tumor stemness, and cancer drug resistance with vulnerability to bitopic mTOR inhibition
Authors: Katsuno Yoko , Meyer Dominique Stephan , Zhang Ziyang , Shokat Kevan M. , Akhurst Rosemary J. , Miyazono Kohei , Derynck Rik
Published: February 2019

Inhibiting mTOR may reverse TGF-β–induced metastatic traits and drug resistance in carcinoma cells.
Tropism and Infectivity of a Seasonal A(H1N1) and a Highly Pathogenic Avian A(H5N1) Influenza Virus in Primary Differentiated Ferret Nasal Epithelial Cell Cultures
Authors: Zeng Hui , Goldsmith Cynthia S. , Kumar Amrita , Belser Jessica A. , Sun Xiangjie , Pappas Claudia , Brock Nicole , Bai Yaohui , Levine Min , Tumpey Terrence M. , Maines Taronna R.
Published: February 2019

Although ferrets serve as an important model of influenza virus infection, much remains unknown about virus-host interactions in this species at the cellular level. The development of differentiated primary cultures of ferret nasal epithelial cells is an important step toward understanding cellular tropism and the mechanisms of influenza virus infection and replication in the airway milieu of this model. Using lectin staining and microscopy techniques, we characterized the sialic acid receptor distribution and the cellular composition of the culture model. We then evaluated the replication of and immune response to human and avian influenza viruses at relevant physiological temperatures. Our findings offer significant insight into this first line of defense against influenza virus infection and provide a model for the evaluation of emerging influenza viruses in a well-controlled
in vitro
environmental setting.
Role of Enteroviral RNA-Dependent RNA Polymerase in Regulation of MDA5-Mediated Beta Interferon Activation
Authors: Kuo Rei-Lin , Chen Chi-Jene , Wang Robert Y. L. , Huang Hsing-I , Lin Ya-Han , Tam Ee-Hong , Tu Wen-Jung , Wu Shang-En , Shih Shin-Ru
Published: February 2019

Infection by enteroviruses causes severe neurological complications in humans. Human enteroviruses possess various mechanisms to suppress the host type I interferon (IFN) response in infected cells to establish viral replication. In the present study, we found that the enteroviral 3D
pol
protein (or RdRP), which is a viral RNA-dependent RNA polymerase for replicating viral RNA, plays a role in the inhibition of MDA5-mediated beta interferon (IFN-β) promoter activation. We further demonstrated that enteroviral 3D
pol
protein interacts with the caspase activation and recruitment domains (CARDs) of MDA5. These findings indicate that enteroviral RdRP functions as an antagonist against the host antiviral response.
HIV Controllers Have Low Inflammation Associated with a Strong HIV-Specific Immune Response in Blood
Authors: Hocini Hakim , Bonnabau Henri , Lacabaratz Christine , Lefebvre Cécile , Tisserand Pascaline , Foucat Emile , Lelièvre Jean-Daniel , Lambotte Olivier , Saez–Cirion Asier , Versmisse Pierre , Thiébaut Rodolphe , Lévy Yves
Published: February 2019

A small minority of HIV-infected patients, called HIV controllers (HIC), maintains spontaneous control of HIV replication. It is therefore important to identify mechanisms that contribute to the control of HIV replication that may have implications for vaccine design. We observed a low inflammation, a downmodulation of natural killer inhibitory cell signaling, and an upregulation of T-cell activation gene expression in the blood of HIC compared to patients under combined antiretroviral treatment. This profile persists following
in vitro
stimulation of peripheral blood mononuclear cells with HIV antigens, and was consistent with functional analyses showing a Th1 and cytotoxic T cell response and a lower production of inflammatory cytokines. These results reveal significant features of HIC that maintain strong HIV-specific immune responses with low levels of inflammation. These findings define the immune status of HIC that is probably associated with the control of viral load.
Genome Sequence of Flavor-Producing Yeast Saprochaete suaveolens NRRL Y-17571
Authors: Lichancová Hana , Hodorová Viktória , Sienkiewicz Karolina , Penir Sarah Mae U. , Afanasyev Philipp , Boceck Dominic , Bonnin Sarah , Hakobyan Siras , Krawczyk Pawel S. , Smyczynska Urszula , Zhivkoplias Erik , Zlatohurska Maryna , Odrzywolski Adrian , Tralle Eugeniusz , Frolova Alina , Pryszcz Leszek P. , Brejová Broňa , Vinař Tomáš , Nosek Jozef
Published: February 2019

Saprochaete suaveolens
is an ascomycetous yeast that produces a range of fruity flavors and fragrances. Here, we report the high-contiguity genome sequence of the ex-holotype strain, NRRL Y-17571 (CBS 152.25).
Draft Genome Sequence of
Trypanosoma equiperdum
Strain IVM-t1
Authors: Davaasuren Batdorj , Yamagishi Junya , Mizushima Daiki , Narantsatsral Sandagdorj , Otgonsuren Davaajav , Myagmarsuren Punsantsogvoo , Battsetseg Badgar , Battur Banzragch , Inoue Noboru , Suganuma Keisuke
Published: February 2019

Trypanosoma equiperdum
primarily parasitizes the genital organs and causes dourine in equidae. We isolated a new
T. equiperdum
strain,
T. equiperdum
IVM-t1, from the urogenital tract of a horse definitively diagnosed as having dourine in Mongolia.
PacBio Genome Sequences of Eight Escherichia albertii Strains Isolated from Humans in the United States
Authors: Lindsey Rebecca L. , Rowe Lori A. , Batra Dhwani , Smith Peyton , Strockbine Nancy A.
Published: February 2019

Escherichia albertii
is an emerging pathogen that is closely related to
Escherichia coli
and can carry some of the same virulence genes as
E. coli
. Here, we report the release of Illumina-corrected PacBio sequences for eight
E. albertii
genomes.
Unusual complication of an Alaskan cruise: thinking outside the box
Authors: Bhandare Deepti , Ruchi Rupam
Published: February 2019

A 69-year-old man with a medical history of hypertension and diabetes presented with altered mental status once he returned from a 14-day Alaskan cruise. An extensive workup for stroke was negative. His physical examination was normal without any focal motor deficits, but he had developed memory loss and paresthesia. He admitted to eating a lot of fish when he was in Alaska. The whole-blood mercury level was found to be elevated. He was managed conservatively and his symptoms resolved completely in a few days. This led to a diagnosis of organic mercury toxicity.
Pharyngocutaneous fistula caused by dried ‘Kombu’ (edible seaweed) after total laryngectomy
Authors: Kusaba Yuki , Miwa Toru , Ise Momoko , Minoda Ryosei
Published: February 2019

The most common early complication after total laryngectomy is pharyngocutaneous fistula (PCF). However, there are no reports of PCF after total laryngectomy caused by ‘Kombu’ (edible seaweed) as a foreign body in the digestive tract. A 68-year-old Japanese man had undergone total laryngectomy 5 years previously. He presented with PCF, neck swelling and pain. Video endoscopy showed that a dark green foreign body obstructed the digestive tract. PCF was successfully treated via emergency surgery comprising abscess drainage, foreign body removal and fistula closure. The foreign body was kombu. Clinicians who perform total laryngectomy should know the potential dangers of consuming hygroscopic food items that can cause bolus obstruction of the upper digestive tract and pharyngeal abscess and perforation.
Health services utilisation and responsiveness profiles in Iran: a provincial household study
Authors: Farahbakhsh Mostafa , Sadeghi Bazargani Homayoun , Saadati Mohammad , Tabrizi Jafar Sadegh , Golestani Mina , Zakery Akram
Published: February 2019

Objective

The aim of this study was to describe health services utilisation and responsiveness in East Azerbaijan province, Iran.

Design

A cross-sectional household study as part of a larger research on primary healthcare system.

Setting

We carried out the study in East Azerbaijan Province, northwest Iran from July to September 2015.

Participants

A total of 1318 households were included.

Results

Most of the participating households had social security health insurance. Heart failure or hypertension care, general outpatient care and arthritis care were the most used services. High services cost and inadequate medicine and medical equipment were introduced to be the main barriers to health services utilisation in Tabriz and province representative sample (PRS), respectively. Health system responsiveness mean score (the maximum is 100) was 33.71±16.15 (95% CI 32.45 to 34.97) in Tabriz and 32.02±14.3 (95% CI 30.9 to 33.13) in PRS, which showed significant difference (p≤0.02).

Conclusions

Differences in the utilisation and responsiveness of health services and distribution of health resources were observed between Tabriz and PRS. Evidently, health system responsiveness in both Tabriz and PRS was at low level. The results demonstrate the need for changing resource distribution policies and employing reactive health policies to response the public health.
Real-time automatic detection system increases colonoscopic polyp and adenoma detection rates: a prospective randomised controlled study
Authors: Wang Pu , Berzin Tyler M , Glissen Brown Jeremy Romek , Bharadwaj Shishira , Becq Aymeric , Xiao Xun , Liu Peixi , Li Liangping , Song Yan , Zhang Di , Li Yi , Xu Guangre , Tu Mengtian , Liu Xiaogang
Published: February 2019

Objective

The effect of colonoscopy on colorectal cancer mortality is limited by several factors, among them a certain miss rate, leading to limited adenoma detection rates (ADRs). We investigated the effect of an automatic polyp detection system based on deep learning on polyp detection rate and ADR.

Design

In an open, non-blinded trial, consecutive patients were prospectively randomised to undergo diagnostic colonoscopy with or without assistance of a real-time automatic polyp detection system providing a simultaneous visual notice and sound alarm on polyp detection. The primary outcome was ADR.

Results

Of 1058 patients included, 536 were randomised to standard colonoscopy, and 522 were randomised to colonoscopy with computer-aided diagnosis. The artificial intelligence (AI) system significantly increased ADR (29.1%vs20.3%, p<0.001) and the mean number of adenomas per patient (0.53vs0.31, p<0.001). This was due to a higher number of diminutive adenomas found (185vs102; p<0.001), while there was no statistical difference in larger adenomas (77vs58, p=0.075). In addition, the number of hyperplastic polyps was also significantly increased (114vs52, p<0.001).

Conclusions

In a low prevalent ADR population, an automatic polyp detection system during colonoscopy resulted in a significant increase in the number of diminutive adenomas detected, as well as an increase in the rate of hyperplastic polyps. The cost–benefit ratio of such effects has to be determined further.

Trial registration number

ChiCTR-DDD-17012221; Results.
Matricidal cavernous aneurysms: a multicenter case series
Authors: Dacus Mallory R , Nickele Chris , Welch Babu G , Ban Vin Shen , Ringer Andrew J , Kim Louis J , Levitt Michael R , Lanzino Giuseppe , Kan Peter , Arthur Adam S
Published: February 2019

Background

Cavernous carotid artery aneurysms (CCAs) represent a unique subset of intracranial aneurysms due to their distinct natural history and the anatomy of the cavernous sinus. Enlarging CCAs can cause elastic compression of the parent internal carotid artery (ICA). We suggest defining aneurysms that cause luminal stenosis of their parent vessels as ‘matricidal aneurysms.’

Though many patients are asymptomatic, presenting symptoms of CCAs include ophthalmoplegia with resulting diplopia, vision changes, pain, ptosis, facial numbness, and cavernous-carotid fistula. Less commonly, patients with CCAs can present with epistaxis, subarachnoid hemorrhage, and—in cases of matricidal aneurysms—ischemia due to stenosis. The proper management of stenosis caused by a matricidal CCA is not well established and may not be intuitive.

Methods

We present a multicenter retrospective case series of patients with matricidal CCAs.

Results

Forty patients with matricidal aneurysms presented with both asymptomatic and symptomatic stenosis. These patients were either treated with conservative medical management, coiling, flow diversion, or endovascular sacrifice of the parent artery. Planned treatment modalities were not executed in 11 cases (28% treatment failure rate). Presenting symptoms, patient outcomes, and follow-up data are presented for all cases.

Conclusion

Matricidal aneurysms require careful consideration and planning. The restricted anatomy of the cavernous sinus can make successful execution of endovascular interventions more difficult. Direct elastic compression of the parent artery does not respond to angioplasty and stenting in the same way atherosclerotic stenosis does. Because of this, planning for the possibility of parent vessel sacrifice is important.
Percentage of progressors in imaging: can we ignore regressors?
Authors: Sepriano Alexandre , Ramiro Sofia , Landewé Robert , Dougados Maxime , van der Heijde Desirée
Published: February 2019

Stopping or preventing structural progression is a goal common to all inflammatory rheumatic diseases. Imaging may capture structural progression across diseases, but is susceptible to measurement error. Progression can be analysed as a continuous change score over time (eg, mean change of the van der Heijde-modified Sharp score) or as a binary change score (eg, percentage of progressors according to the modified New York criteria). Here, we argue that the former takes measurement error into account while the latter ignores it, which may lead to spurious conclusions. We will argue that assumptions underlying commonly used binary definitions of progression are false and we propose a method that incorporates (inevitable) measurement error.
Geology of the Chang 7 Member oil shale of the Yanchang Formation of the Ordos Basin in central north China
Authors: Yunlai Bai , Yuhu Ma
Published: February 2019

We present a review of the Chang 7 Member oil shale, which occurs in the middle–late Triassic Yanchang Formation of the Ordos Basin in central north China. The oil shale has a thickness of 28 m (average), an area of around 30 000 km
2
and a Ladinian age. It is mainly brown-black to black in colour with a laminar structure. It is characterized by average values of 18 wt% TOC (total organic carbon), 8 wt% oil yield, a 8.35 MJ kg
−1
calorific value, 400 kg t
−1
hydrocarbon productivity and kerogen of type I–II
1
, showing a medium quality. On average, it comprises 49% clay minerals, 29% quartz, 16% feldspar and some iron oxides, which is close to the average mineral composition of global shale. The total SiO
2
and Al
2
O
3
comprise 63.69 wt% of the whole rock, indicating a medium ash type. The Sr/Ba is 0.33, the V/Ni is 7.8, the U/Th is 4.8 and the FeO/Fe
2
O
3
is 0.5, indicating formation in a strongly reducing, freshwater or low-salinity sedimentary environment. Multilayered intermediate-acid tuff is developed in the basin, which may have promoted the formation of the oil shale. The Ordos Basin was formed during the northwards subduction of the Qinling oceanic plate during the Ladinian–Norian in a back-arc basin context. The oil shale of the Ordos Basin has a large potential for hydrocarbon generation.

Supplementary material:
Tables of oil-shale geochemical composition, proximate and organic matter analyses from the Chang 7 Member oil shale, the Ordos Basin, Central north China are available at
https://doi.org/10.6084/m9.figshare.c.4411703
A multidisciplinary approach for the quantitative provenance analysis of siltstone: Mesozoic Mandawa Basin, southeastern Tanzania
Authors: Caracciolo L. , Andò S. , Vermeesch P. , Garzanti E. , McCabe R. , Barbarano M. , Paleari C. , Rittner M. , Pearce T.
Published: February 2019

This paper shows how heavy minerals and single-grain varietal studies can be conducted on silt (representing
c.
50% of world's sediments) sediments to obtain quantitative data as efficiently as for sand-sized sediments. The analytical workflows include heavy mineral separation using a wide grain-size window (15–355 μ) analysed through integrated optical analysis, Raman spectroscopy, QEMSCAN microscopy and U–Pb dating of detrital zircon. Upper Jurassic–Cretaceous silt-sized sediments from the Mandawa Basin of central-southern Tanzania have been selected for the scope of this research. Raman-aided heavy mineral analysis reveals garnet and apatite to be the most common minerals together with durable zircon, tourmaline and subordinate rutile. Accessory but diagnostic phases are titanite, staurolite, epidote and monazite. Etch pits on garnet and cockscomb features on staurolite document the significant effect of diagenesis on the pristine heavy mineral assemblage. Multivariate statistical analysis highlights a close association among durable minerals (zircon, tourmaline and rutile, ZTR) while garnet and apatite plot alone reflecting independence between the three groups of variables with garnet increasing in Jurassic samples. Raman data for garnet end-member analysis document different associations between Jurassic (richer in A, Bi and Bii types) and Cretaceous (dominant A, Ci and Cii types) samples. U–Pb dating of detrital zircon and their statistical integration with the above-mentioned datasets provide further insights into changes in provenance and/or drainage systems. Metamorphic rocks of the early and late Pan-African orogeny terranes of the Mozambique Belt and those of the Irumide Belt acted as main source of sediment during the Jurassic. Cretaceous sediments record a broadening of the drainage system reaching as far as the Usagran–Ubendian Belt and the Tanzanian Archean Craton.
Machine Learning for Survival Analysis
Authors: Wang Ping , Li Yan , Reddy Chandan K.
Published: February 2019

Survival analysis is a subfield of statistics where the goal is to analyze and model data where the outcome is the time until an event of interest occurs. One of the main challenges in this context is the presence of instances whose event outcomes become unobservable after a certain time point or when some instances do not experience any event during the monitoring period. This so-calledcensoringcan be handled most effectively using survival analysis techniques. Traditionally, statistical approaches have been widely developed in the literature to overcome the issue of censoring. In addition, many machine learning algorithms have been adapted to deal with such censored data and tackle other challenging problems that arise in real-world data. In this survey, we provide a comprehensive and structured review of the statistical methods typically used and the machine learning techniques developed for survival analysis, along with a detailed taxonomy of the existing methods. We also discuss several topics that are closely related to survival analysis and describe several successful applications in a variety of real-world application domains. We hope that this article will give readers a more comprehensive understanding of recent advances in survival analysis and offer some guidelines for applying these approaches to solve new problems arising in applications involving censored data.
A Survey on Brain Biometrics
Authors: Gui Qiong , Ruiz-Blondet Maria V. , Laszlo Sarah , Jin Zhanpeng
Published: February 2019

Brainwaves, which reflect brain electrical activity and have been studied for a long time in the domain of cognitive neuroscience, have recently been proposed as a promising biometric approach due to their unique advantages of confidentiality, resistance to spoofing/circumvention, sensitivity to emotional and mental state, continuous nature, and cancelability. Recent research efforts have explored many possible ways of using brain biometrics and demonstrated that they are a promising candidate for more robust and secure personal identification and authentication. Although existing research on brain biometrics has obtained some intriguing insights, much work is still necessary to achieve a reliable ready-to-deploy brain biometric system. This article aims to provide a detailed survey of the current literature and outline the scientific work conducted on brain biometric systems. It provides an up-to-date review of state-of-the-art acquisition, collection, processing, and analysis of brainwave signals, publicly available databases, feature extraction and selection, and classifiers. Furthermore, it highlights some of the emerging open research problems for brain biometrics, including multimodality, security, permanence, and stability.
Putting Question-Answering Systems into Practice
Authors: Kratzwald Bernhard , Feuerriegel Stefan
Published: February 2019

Traditional information retrieval (such as that offered by web search engines) impedes users with information overload from extensive result pages and the need to manually locate the desired information therein. Conversely, question-answering systems change how humans interact with information systems: users can now ask specific questions and obtain a tailored answer—both conveniently in natural language. Despite obvious benefits, their use is often limited to an academic context, largely because of expensive domain customizations, which means that the performance in domain-specific applications often fails to meet expectations. This article proposes cost-efficient remedies: (i) we leverage metadata through a filtering mechanism, which increases the precision of document retrieval, and (ii) we develop a novel fuse-and-oversample approach for transfer learning to improve the performance of answer extraction. Here, knowledge is inductively transferred from related, yet different, tasks to the domain-specific application, while accounting for potential differences in the sample sizes across both tasks. The resulting performance is demonstrated with actual use cases from a finance company and the film industry, where fewer than 400 question-answer pairs had to be annotated to yield significant performance gains. As a direct implication to management, this presents a promising path to better leveraging of knowledge stored in information systems.
Leaf Senescence: Systems and Dynamics Aspects
Authors: Woo Hye Ryun , Kim Hyo Jung , Lim Pyung Ok , Nam Hong Gil
Published: February 2019

Leaf senescence is an important developmental process involving orderly disassembly of macromolecules for relocating nutrients from leaves to other organs and is critical for plants’ fitness. Leaf senescence is the response of an intricate integration of various environmental signals and leaf age information and involves a complex and highly regulated process with the coordinated actions of multiple pathways. Impressive progress has been made in understanding how senescence signals are perceived and processed, how the orderly degeneration process is regulated, how the senescence program interacts with environmental signals, and how senescence regulatory genes contribute to plant productivity and fitness. Employment of systems approaches using omics-based technologies and characterization of key regulators have been fruitful in providing newly emerging regulatory mechanisms. This review mainly discusses recent advances in systems understanding of leaf senescence from a molecular network dynamics perspective. Genetic strategies for improving the productivity and quality of crops are also described.
Early Lessons from the Implementation of Genomic Medicine Programs
Authors: Williams Marc S.
Published: February 2019

Massively parallel sequencing is emerging from research settings into clinical practice, helping the vision of precision medicine to become a reality. The most successful applications are using the tools of implementation science within the framework of the learning health-care system. This article examines the application of massively parallel sequencing to four clinical scenarios: pharmacogenomics, diagnostic testing, somatic testing for molecular tumor characterization, and population screening. For each application, it highlights an exemplar program to illustrate the enablers and challenges of implementation. International examples are also presented. These early lessons will allow other programs to account for these factors, helping to accelerate the implementation of precision medicine and health.
Regulation of IL-17A and implications for TGF-β1 comodulation of airway smooth muscle remodeling in severe asthma
Authors: Evasovic Jon M. , Singer Cherie A.
Published: February 2019

Severe asthma develops as a result of heightened, persistent symptoms that generally coincide with pronounced neutrophilic airway inflammation. In individuals with severe asthma, symptoms are poorly controlled by high-dose inhaled glucocorticoids and often lead to elevated morbidity and mortality rates that underscore the necessity for novel drug target identification that overcomes limitations in disease management. Many incidences of severe asthma are mechanistically associated with T helper 17 (TH17) cell-derived cytokines and immune factors that mediate neutrophilic influx to the airways. TH17-secreted interleukin-17A (IL-17A) is an independent risk factor for severe asthma that impacts airway smooth muscle (ASM) remodeling. TH17-derived cytokines and diverse immune mediators further interact with structural cells of the airway to induce pathophysiological processes that impact ASM functionality. Transforming growth factor-β1 (TGF-β1) is a pivotal mediator involved in airway remodeling that correlates with enhanced TH17 activity in individuals with severe asthma and is essential to TH17 differentiation and IL-17A production. IL-17A can also reciprocally enhance activation of TGF-β1 signaling pathways, whereas combined TH1/TH17 or TH2/TH17 immune responses may additively impact asthma severity. This review seeks to provide a comprehensive summary of cytokine-driven T cell fate determination and TH17-mediated airway inflammation. It will further review the evidence demonstrating the extent to which IL-17A interacts with various immune factors, specifically TGF-β1, to contribute to ASM remodeling and altered function in TH17-driven endotypes of severe asthma.
Epidermal growth factor receptor paracrine upregulation in idiopathic pulmonary fibrosis fibroblasts is blocked by nintedanib
Authors: Epstein Shochet Gali , Brook Elizabetha , Eyal Omer , Edelstein Evgeny , Shitrit David
Published: February 2019

Although present in normal cells, epidermal growth factor receptor (EGFR) is overexpressed in a variety of tumors and has been associated with decreased survival. Because activated fibroblasts are considered key effectors in fibrosis and because metastatic and fibrotic processes were shown to share similar signaling pathways, we investigated the contribution of EGFR signaling to idiopathic pulmonary fibrosis (IPF) progression in lung fibroblasts derived from patients with IPF (IPF-HLF). EGFR expression and EGFR-related signaling were evaluated by Western blot and immunohistochemistry. Supernatants (SN) from cultured IPF-HLF and N-HLF were added to N-HLF, and their effect on cell phenotype was tested. Growth factor levels in the SN were measured by ELISA-based arrays. EGFR activity was blocked by erlotinib (Tarceva, 0.1–0.5 µM). Expression of EGFR, phosphorylated (p)EGFR-1068 and pAkt-473 was significantly higher in IPF-HLF compared with lung fibroblasts from control donors (N-HLF) ( P < 0.05). Apparent expression of p/total EGFR and pAkt-473 was found in the myofibroblastic foci of IPF patients. Erlotinib significantly inhibited IPF-HLF but not N-HLF proliferation. IPF-HLF-SN elevated N-HLF cell number, viability, EGFR expression, and pAkt-473 and ERK1/2 phosphorylation ( P < 0.05). Because high basic fibroblast growth factor levels were found in the IPF-HLF-SN, nintedanib (10–100 nM) was used to inhibit fibroblast growth factor receptor (FGFR) activation. Unlike erlotinib, nintedanib completely blocked IPF-HLF-SNs’ effects on the N-HLF cells in a concentration-dependent manner. In summary, IPF-HLF paracrine signaling elevates EGFR expression, which in turn, affects N-HLF survival. The FGF-EGFR interplay facilitates cellular responses that could potentially promote fibrotic disease. This interplay was successfully blocked by nintedanib.
CCR5 is a required signaling receptor for macrophage expression of inflammatory genes in response to viral double-stranded RNA
Authors: Shaheen Zachary R. , Christmann Benjamin S. , Stafford Joshua D. , Moran Jason M. , Buller R. Mark L. , Corbett John A.
Published: February 2019

Double-stranded (ds) RNA, both synthetic and produced during virus replication, rapidly stimulates MAPK and NF-κB signaling that results in expression of the inflammatory genes inducible nitric oxide synthase, cyclooxygenase 2, and IL-1β by macrophages. Using biochemical and genetic approaches, we have identified the chemokine ligand-binding C-C chemokine receptor type 5 (CCR5) as a cell surface signaling receptor required for macrophage expression of inflammatory genes in response to dsRNA. Activation of macrophages by synthetic dsRNA does not require known dsRNA receptors, as poly(inosinic:cytidylic) acid [poly(I:C)] activates signaling pathways leading to expression of inflammatory genes to similar levels in wild-type and Toll-like receptor 3- or melanoma differentiation antigen 5-deficient macrophages. In contrast, macrophage activation in response to poly(I:C) is attenuated in macrophages isolated from mice lacking CCR5. These findings support a role for CCR5 as a cell surface signaling receptor that participates in activation of inflammatory genes in macrophages in response to the viral dsRNA mimetic poly(inosinic:cytidylic) acid by pathways that are distinct from classical dsRNA receptor-mediated responses.
Podocyte-specific expression of Cre recombinase promotes glomerular basement membrane thickening
Authors: Balkawade Rohan S. , Chen Chao , Crowley Michael R. , Crossman David K. , Clapp William L. , Verlander Jill W. , Marshall Caroline B.
Published: February 2019

Conditional gene targeting using Cre recombinase has offered a powerful tool to modify gene function precisely in defined cells/tissues and at specific times. However, in mammalian cells, Cre recombinase can be genotoxic. The importance of including Cre-expressing control mice to avoid misinterpretation and to maximize the validity of the experimental results has been increasingly recognized. While studying the role of podocytes in the pathogenesis of glomerular basement membrane (GBM) thickening, we used Cre recombinase driven by the podocyte-specific podocin promoter (NPHS2-Cre) to generate a conditional knockout. By conventional structural and functional measures (histology by periodic acid-Schiff staining, albuminuria, and plasma creatinine), we did not detect significant differences between NPHS2-Cre transgenic and wild-type control mice. However, surprisingly, the group that expressed Cre transgene alone developed signs of podocyte toxicity, including marked GBM thickening, loss of normal foot process morphology, and reduced Wilms tumor 1 expression. GBM thickening was characterized by altered expression of core structural protein laminin isoform α5β2γ1. RNA sequencing analysis of extracted glomeruli identified 230 genes that were significant and differentially expressed (applying a q < 0.05-fold change ≥ ±2 cutoff) in NPHS2-Cre mice compared with wild-type control mice. Many biological processes were reflected in the RNA sequencing data, including regulation of the extracellular matrix and pathways related to apoptosis and cell death. This study highlights the importance of including the appropriate controls for potential Cre-mediated toxicity in conditional gene-targeting experiments. Indeed, omitting the Cre transgene control can result in critical errors during interpretation of experimental data.
Spreading depolarization and neuronal damage or survival in mouse neocortical brain slices immediately and 12 hours following middle cerebral artery occlusion
Authors: Petrin Dylan , Gagolewicz Peter J. , Mehder Rasha H. , Bennett Brian M. , Jin Albert Y. , Andrew R. David
Published: February 2019

Whereas many studies have examined the properties of the compromised neocortex in the first several days following ischemia, there is less information regarding the initial 12 h poststroke. In this study we examined live mouse neocortical slices harvested immediately and 12 h after a 30-min middle cerebral artery occlusion (MCAo). We compared nonischemic and ischemic hemispheres with regard to the propensity for tissue swelling and for generating spreading depolarization (SD), as well as evoked synaptic responses and single pyramidal neuron electrophysiological properties. We observed spontaneous SD in 7% of slices on the nonstroked side and 25% in the stroked side following the 30-min MCAo. Spontaneous SD was rare in 12-h recovery slices. The region of the ischemic core and surround in slices was not susceptible to SD induced by oxygen and glucose deprivation. At the neuronal level, neocortical gray matter is surprisingly unaltered in brain slices harvested immediately poststroke. However, by 12 h, the fields of pyramidal and striatal neurons that comprise the infarcted core are electrophysiologically silent because the majority are morphologically devastated. Yet, there remains a subset of diffusely distributed “healthy” pyramidal neurons in the core at 12 h post-MCAo that persist for days poststroke. Their intact electrophysiology and dendritic morphology indicate a surprisingly selective resilience to stroke at the neuronal level.

NEW & NOTEWORTHY It is generally accepted that the injured core region of the brain resulting from a focal stroke contains no functioning neurons. Our study shows that some neurons, although surrounded by devastated neighbors, can maintain their structure and electrical activity. This surprising finding raises the possibility of discovering how these neurons are protected to pinpoint new strategies for reducing stroke injury.
Neural signatures of reward and sensory error feedback processing in motor learning
Authors: Palidis Dimitrios J. , Cashaback Joshua G. A. , Gribble Paul L.
Published: February 2019

At least two distinct processes have been identified by which motor commands are adapted according to movement-related feedback: reward-based learning and sensory error-based learning. In sensory error-based learning, mappings between sensory targets and motor commands are recalibrated according to sensory error feedback. In reward-based learning, motor commands are associated with subjective value, such that successful actions are reinforced. We designed two tasks to isolate reward- and sensory error-based motor adaptation, and we used electroencephalography in humans to identify and dissociate the neural correlates of reward and sensory error feedback processing. We designed a visuomotor rotation task to isolate sensory error-based learning that was induced by altered visual feedback of hand position. In a reward learning task, we isolated reward-based learning induced by binary reward feedback that was decoupled from the visual target. A fronto-central event-related potential called the feedback-related negativity (FRN) was elicited specifically by binary reward feedback but not sensory error feedback. A more posterior component called the P300 was evoked by feedback in both tasks. In the visuomotor rotation task, P300 amplitude was increased by sensory error induced by perturbed visual feedback and was correlated with learning rate. In the reward learning task, P300 amplitude was increased by reward relative to nonreward and by surprise regardless of feedback valence. We propose that during motor adaptation the FRN specifically reflects a reward-based learning signal whereas the P300 reflects feedback processing that is related to adaptation more generally.

NEW & NOTEWORTHY We studied the event-related potentials evoked by feedback stimuli during motor adaptation tasks that isolate reward- and sensory error-based learning mechanisms. We found that the feedback-related negativity was specifically elicited by binary reward feedback, whereas the P300 was observed in both tasks. These results reveal neural processes associated with different learning mechanisms and elucidate which classes of errors, from a computational standpoint, elicit the feedback-related negativity and P300.
Quantification of vibrissal mechanical properties across the rat mystacial pad
Authors: Yang Anne En-Tzu , Belli Hayley M. , Hartmann Mitra J. Z.
Published: February 2019

Recent work has quantified the geometric parameters of individual rat vibrissae (whiskers) and developed equations that describe how these parameters vary as a function of row and column position across the array. This characterization included a detailed quantification of whisker base diameter and arc length as well as the geometry of the whisker medulla. The present study now uses these equations for whisker geometry to quantify several properties of the whisker that govern its mechanical behavior. We first show that the average density of a whisker is lower in its proximal region than in its distal region. This density variation appears to be largely attributable to the presence of the whisker cuticle rather than the medulla. The density variation has very little effect on the center of mass of the whisker. We next show that the presence of the medulla decreases the deflection of the whisker under its own weight and also decreases its mass moment of inertia while sacrificing <1% stiffness at the whisker base compared with a solid whisker. Finally, we quantify two dimensionless parameters across the array. First, the deflection-to-length ratio decreases from caudal to rostral: caudal whiskers are longer but deflect more under their own weight. Second, the nondimensionalized radius of gyration is approximately constant across the array, which may simplify control of whisking by the intrinsic muscles. We anticipate that future work will exploit the mechanical properties computed in the present study to improve simulations of the mechanosensory signals associated with vibrissotactile exploratory behavior.

NEW & NOTEWORTHY The mechanical signals transmitted by a whisker depend critically on its geometry. We used measurements of whisker geometry and mass to quantify the center of mass, mass moment of inertia, radius of gyration, and deflection under gravity of the whisker. We describe how variations in these quantities across the array could enhance sensing behaviors while reducing energy costs and simplifying whisking control. Most importantly, we provide derivations for these quantities for use in future simulation work.
The Orphan Nuclear Receptors Steroidogenic Factor-1 and Liver Receptor Homolog-1: Structure, Regulation, and Essential Roles in Mammalian Reproduction
Authors: Meinsohn Marie-Charlotte , Smith Olivia E. , Bertolin Kalyne , Murphy Bruce D.
Published: February 2019

Nuclear receptors are intracellular proteins that act as transcription factors. Proteins with classic nuclear receptor domain structure lacking identified signaling ligands are designated orphan nuclear receptors. Two of these, steroidogenic factor-1 (NR5A1, also known as SF-1) and liver receptor homolog-1 (NR5A2, also known as LRH-1), bind to the same DNA sequences, with different and nonoverlapping effects on targets. Endogenous regulation of both is achieved predominantly by cofactor interactions. SF-1 is expressed primarily in steroidogenic tissues, LRH-1 in tissues of endodermal origin and the gonads. Both receptors modulate cholesterol homeostasis, steroidogenesis, tissue-specific cell proliferation, and stem cell pluripotency. LRH-1 is essential for development beyond gastrulation and SF-1 for genesis of the adrenal, sexual differentiation, and Leydig cell function. Ovary-specific depletion of SF-1 disrupts follicle development, while LRH-1 depletion prevents ovulation, cumulus expansion, and luteinization. Uterine depletion of LRH-1 compromises decidualization and pregnancy. In humans, SF-1 is present in endometriotic tissue, where it regulates estrogen synthesis. SF-1 is underexpressed in ovarian cancer cells and overexpressed in Leydig cell tumors. In breast cancer cells, proliferation, migration and invasion, and chemotherapy resistance are regulated by LRH-1. In conclusion, the NR5A orphan nuclear receptors are nonredundant factors that are crucial regulators of a panoply of biological processes, across multiple reproductive tissues.