bluuebunny/crossref_metadata_2025 huggingface dataset:
Recovery Trajectories of Child and Family Outcomes Following Online Family Problem-Solving Therapy for Children and Adolescents after Traumatic Brain Injury
Authors: Wade Shari L. , Fisher Allison P. , Kaizar Eloise E. , Yeates Keith O. , Taylor H. Gerry , Zhang Nanhua
Published: August 2019

Objectives: We conducted joint analyses from five randomized clinical trials (RCTs) of online family problem-solving therapy (OFPST) for children with traumatic brain injury (TBI) to identify child and parent outcomes most sensitive to OFPST and trajectories of recovery over time. Methods: We examined data from 359 children with complicated mild to severe TBI, aged 5–18, randomized to OFPST or a control condition. Using profile analyses, we examined group differences on parent-reported child (internalizing and externalizing behavior problems, executive function behaviors, social competence) and family outcomes (parental depression, psychological distress, family functioning, parent–child conflict). Results: We found a main effect for measure for both child and family outcomes [F(3, 731) = 7.35, p < .001; F(3, 532) = 4.79, p = .003, respectively], reflecting differing degrees of improvement across measures for both groups. Significant group-by-time interactions indicated that children and families in the OFPST group had fewer problems than controls at both 6 and 18 months post baseline [t(731) = −5.15, p < .001, and t(731) = −3.90, p = .002, respectively, for child outcomes; t(532) = −4.81, p < .001, and t(532) = −3.80, p < .001, respectively, for family outcomes]. Conclusions: The results suggest limited differences in the measures’ responsiveness to treatment while highlighting OFPST’s utility in improving both child behavior problems and parent/family functioning. Group differences were greatest at treatment completion and after extended time post treatment.
Chester Barnard revisited: spontaneous orders and the firm
Authors: Walsh Aidan , Brady Malcolm
Published: August 2019

That governance within the firm is deliberate, conscious and hierarchical, based on authority is considered almost axiomatic. Chester Barnard is cited as an early theorist of this view. In this short article we review Barnard's original theory of authority, his later work and his private correspondence with F. A. Hayek, Michael Polanyi, Bertrand de Jouvenal and others. We show that Barnard focused in his later thinking less on authority and more on ‘responsibility’ and on the spontaneous nature of coordination within the firm, argued for ‘invisible hand’ explanations of coordination within the firm and compared coordination within the firm to market coordination. We use this information to produce novel insights into the work of Chester Barnard and also to demonstrate that his insights into the inner workings of firms is still not completely understood or reflected in the literature on the firm.
CUT ELIMINATION IN HYPERSEQUENT CALCULUS FOR SOME LOGICS OF LINEAR TIME
Authors: INDRZEJCZAK ANDRZEJ
Published: August 2019

This is a sequel article to [10] where a hypersequent calculus (HC) for some temporal logics of linear frames includingKt4.3and its extensions for dense and serial flow of time was investigated in detail. A distinctive feature of this approach is that hypersequents are noncommutative, i.e., they are finite lists of sequents in contrast to other hypersequent approaches using sets or multisets. Such a system in [10] was proved to be cut-free HC formalization of respective logics by means of semantical argument. In this article we present an equivalent variant of this calculus for which a constructive syntactical proof of cut elimination is provided.
THE ELIMINATION OF ATOMIC CUTS AND THE SEMISHORTENING PROPERTY FOR GENTZEN’S SEQUENT CALCULUS WITH EQUALITY
Authors: PARLAMENTO FRANCO , PREVIALE FLAVIO
Published: August 2019

We study various extensions of Gentzen’s sequent calculus obtained by adding rules for equality. One of them is singled out as particularly natural and shown to satisfy full cut elimination, namely, also atomic cuts can be eliminated. Furthermore we tell apart the extensions that satisfy full cut elimination from those that do not and establish a strengthened form of the nonlenghtening property of Lifschitz and Orevkov.
Broadleaf weed control in rain-fed chickpea
Authors: Shahbazi Saeed , Diyanat Marjan , Mahdavi Sareh , Samadi Soheida
Published: August 2019

Weeds are among the main limitations on chickpea production in Iran. The efficacy of herbicide treatments including linuron PPI, imazethapyr PPI, PRE, and POST, pendimethalin PPI and POST, bentazon POST, pyridate POST, and oxadiazon POST along with one or two hand weedings were evaluated for weed control and yield response in rain-fed chickpea in Aleshtar, Lorestan, Iran in 2015 and 2016. Wild safflower, threehorn bedstraw, wild mustard, and hoary cress were the predominant weed species in both experimental years. Total weed dry biomass in weedy check plots averaged 187 and 238 g m−2in 2015 and 2016, respectively, and weed density and biomass were reduced in all treatments compared to the weedy check in both years. Treatments composed of pyridate followed by one hand weeding or imazethapyr POST followed by two hand weedings resulted in the lowest weed biomass. The presence of weeds reduced yield by 74% and 66% in the weedy check plots compared to the weed-free control plots in 2015 and 2016, respectively. Application of oxadiazon, bentazon, and imazethapyr PPI, PRE, and POST resulted in lower chickpea yields. All herbicides tested injured chickpea slightly, with pyridate causing the least injury.
Impacts of Hydrological Changes on Nutrient Transport From Diffuse Sources in a Rural River Basin, Western Japan
Authors: Ide Jun'ichiro , Takeda Ikuo , Somura Hiroaki , Mori Yasushi , Sakuno Yuji , Yone Yasumichi , Takahashi Erina
Published: August 2019

Increased frequency of heavy rainfall caused by climate change may affect nutrient transport from forests and agricultural lands into downstream rivers. However, little information is available on how the effects of land cover on nutrient concentrations in the downstream rivers change depending on hydrological conditions. To elucidate this, we investigated the effects of changes in precipitation and river discharge on the relationship between river nutrient concentrations (total nitrogen, total phosphorus, nitrate, and phosphate) and land cover in eight subbasins of the Hii River basin, western Japan. We hypothesized that coniferous forests and agricultural lands including poorly managed ones, which require thinning and fertilizer management, respectively, contribute to increases in nutrient concentrations in downstream rivers during storms. Linear mixed‐effects model analyses based on 18‐year observation data were used for testing the hypothesis. Results revealed that the slopes of the multiple regression analysis between nutrient concentrations and coniferous and broad‐leaved forest area ratios were negative and decreased with increasing daily precipitation. This suggests that forests contributed to the dilution of river nutrient concentrations during storms regardless of whether they were coniferous or broad leaved. In contrast, the slope of regression between nutrient concentrations and agricultural area ratio revealed the opposite trend, indicating that even a small percentage of agricultural area makes a large contribution to increases in nutrient concentrations as precipitation increases. Our results imply that storm runoff in response to rainfall results in an elevated supply of nitrogen and phosphorus attached to arable soils to the river.
Transportation of Diazotroph Community From the Upstream to Downstream of the Kuroshio
Authors: Cheung Shunyan , Suzuki Koji , Xia Xiaomin , Liu Hongbin
Published: August 2019

The Kuroshio is a strong western boundary current in the North Pacific, in which N2 fixation is an important source of new nitrogen. In order to understand the dynamics of diazotrophs in the Kuroshio, we used 454‐pyrosequencing of nifH gene amplicons to unravel and compare the diazotroph communities along the main path of the Kuroshio (23.44° N, 121.99° E–34.3° N, 140.1° E) with its adjacent waters. The diazotroph communities in the geographically distanced stations along the Kuroshio mainstream were highly similar, while those in the Kuroshio adjacent waters were highly varied, indicated that diazotroph communities were actively transported in the Kuroshio. Along the Kuroshio, the UCYN‐A1, UCYN‐C, and Gamma‐A were rather evenly distributed along the Kuroshio, whereas the UCYN‐A2 and Trichodesmium were mainly distributed in the Kuroshio upstream. The diazotroph communities shifted from cyanobacteria dominated in the Kuroshio upstream to proteobacteria (mainly Bradyrhizobium and sulfate‐reducing bacteria) dominated in the downstream. Among all cyanobacterial diazotrophs detected, UCYN‐A1 was the most sustained group in the Kuroshio with >103 gene copies per L and that may explain its extended distribution to higher latitude regions as compared with other cyanobacterial diazotrophs. Considering that the Kuroshio is a hot spot of unicellular cyanobacterial diazotrophs, we have adopted DNA‐directed RNA polymerase subunit beta (rpoC1) gene as a biomarker to further explore their phylogeny. Comparing the data set of nifH and rpoC1 gene fragments, we provided new insights into the phylogeny of the recently defined UCYN‐B2 and poorly understood UCYN‐C groups.
Dripwater and Calcite Geochemistry Variations in a Monitored Bahamas Cave
Authors: Arienzo Monica M. , Mehterian Sevag , Swart Peter K. , Broad Kenneth , Kakuk Brian
Published: August 2019

A cave‐monitoring study in Hatchet Bay Cave on the island of Eleuthera, Bahamas, has examined the origins of variations in oxygen and carbon isotopic and minor element composition in cave calcites. Every 3 to 8 months, between 2012 and 2016, temperature, humidity, cave air (δ13CCO2), dripwaters (δ18O and δ2H values, and Ca, Sr, and Mg concentrations), and the chemical composition of precipitating calcite (δ18O and δ13C values, and Ca, Sr, and Mg concentrations) were analyzed in two rooms in the cave. Results from the elemental analyses show that throughout the cave prior calcite precipitation was a driver of the elemental chemistry of the precipitated calcites. In addition, cave calcites show that δ13C and δ18O values were positively correlated with Mg/Ca ratios. The Mg/Ca ratios were also positively correlated with lower calcite precipitation rates. Therefore, water/rock interactions may also influence δ13C and δ18O values and Mg/Ca ratios of the calcite. Differences were observed between the two rooms, with the Main Room of the cave exhibiting increased prior calcite precipitation, more ventilation, lower calcite precipitation rates, and δ18O values, which were farther from equilibrium when compared to the more isolated portion of the cave. These results also validated previous interpretations from Pleistocene stalagmites collected from a nearby Bahamian cave suggesting that a positive covariation between Mg/Ca and δ13C values reflects water/rock interactions.
Evidence of Changes of Seismic Properties in the Entire Crust Beneath Japan After the Mw 9.0, 2011 Tohoku‐oki Earthquake
Authors: Wang Qing‐Yu , Campillo Michel , Brenguier Florent , Lecointre Albanne , Takeda Tetsuya , Hashima Akinori
Published: August 2019

Studies of mechanical responses of the Earth crust to large earthquakes can provide us with unique insights into the processes of stress buildup and release. As a complement to geodetic methods that derive crustal strain dynamics from surface observations (e.g., GPS, InSAR), noise‐based seismic velocity monitoring directly probes the mechanical state of the crust, at depth and continuously in time. We investigate the responses of the crust to the Mw 9.0, 2011 Tohoku‐oki earthquake. In addition to the Hi‐net short‐period sensors, we use Hi‐net tiltmeters as long‐period seismometers (8–50 s) to sample the crust below 5 km in depth. The spatial distribution of the strong velocity decreases at short periods appears to be limited to the region of strong ground shaking induced by the 2011 Tohoku‐oki earthquake, while the long‐period velocity changes correlate well with the modeled static strain induced by viscoelastic relaxation and afterslip at depth. Amplitudes of coseismic velocity changes decrease with increasing depth. The temporal evolution of velocity changes in different period bands shows that the maximum drops in the velocity at long periods are delayed in time with respect to the occurrence of the Tohoku‐oki earthquake. The inversion of seismic velocity changes at depth illustrates how S wave velocities evolve down to 40 km at a regional scale after a major earthquake.
Moored Observations of Transport in the Solomon Sea
Authors: Alberty Marion , Sprintall Janet , MacKinnon Jennifer , Germineaud Cyril , Cravatte Sophie , Ganachaud Alexandre
Published: August 2019

The Solomon Sea is a marginal sea in the western Pacific warm pool that contains the South Pacific low latitude western boundary currents. These low latitude western boundary currents chiefly exit the Solomon Sea through three channels (Vitiaz Strait, St. George's Channel, and Solomon Strait) and serve as the primary source water for the Equatorial Undercurrent. Simulations have shown that transport partitioning between the straits determines the water mass structure of the Equatorial Undercurrent, but the relative contributions of transport through each strait have not been observed before. As part of the Southwest Pacific Ocean Circulation and Climate Experiment, an array of moorings was deployed simultaneously in the three outflow channels of the Solomon Sea from July 2012 until March 2014 to resolve transport and water properties in each strait. Above deep isopycnals (σ0 ≤ 27.5), Vitiaz and Solomon Straits account for 54.2% and 36.2% of the mean transport, respectively, with the remaining 9.6% exiting through St. George's Channel. The strongest subinertial transport variability is observed in Solomon Strait and dominates total Solomon Sea transport variability, and a significant fraction of this variability is at intraseasonal time scales. Finally, a previously unobserved deep current at 1,500‐m depth is found to enter the Solomon Sea through Solomon Strait, with a deployment‐mean transport of 4.6 Sv (Sv ≡106 m3/s).
A protective mechanism of probiotic Lactobacillus against hepatic steatosis via reducing host intestinal fatty acid absorption
Authors: Jang Hye Rim , Park Hyun-Jun , Kang Dongwon , Chung Hayung , Nam Myung Hee , Lee Yeonhee , Park Jae-Hak , Lee Hui-Young
Published: August 2019

The gut microbiome has been known to contribute up to ~30% of the energy absorption of the host. Although various beneficial mechanisms of probiotics have been suggested for non-alcoholic fatty liver disease (NAFLD), whether and which probiotics impact the host’s intestinal energy absorption have not yet been quantitatively studied. Here, we suggest a novel mechanism of probiotics against NAFLD, in which Lactobacillus rhamnosus GG, the most common probiotic, shares intestinal fatty acids and prevents the development of diet-induced hepatic steatosis. By using quantitative methods (radioactive tracers and LC–MS) under both in vitro and in vivo conditions, we found that bacteria and hosts competed for fatty acid absorption in the intestine, resulting in decreased weight gain, body fat mass, and hepatic lipid accumulation without differences in calorie intake and excretion in mice fed the probiotic bacteria.
Metasurface interferometry toward quantum sensors
Authors: Georgi Philip , Massaro Marcello , Luo Kai-Hong , Sain Basudeb , Montaut Nicola , Herrmann Harald , Weiss Thomas , Li Guixin , Silberhorn Christine , Zentgraf Thomas
Published: August 2019

Optical metasurfaces open new avenues for the precise wavefront control of light for integrated quantum technology. Here, we demonstrate a hybrid integrated quantum photonic system that is capable of entangling and disentangling two-photon spin states at a dielectric metasurface. Via the interference of single-photon pairs at a nanostructured dielectric metasurface, a path-entangled two-photon NOON state with circular polarization that exhibits a quantum HOM interference visibility of 86 ± 4% is generated. Furthermore, we demonstrate nonclassicality andphase sensitivity in a metasurface-based interferometer with a fringe visibility of 86.8 ± 1.1% in the coincidence counts. This high visibility proves the metasurface-induced path entanglement inside the interferometer. Our findings provide a promising way to develop hybrid-integrated quantum technology operating in the high-dimensional mode space in various applications, such as imaging, sensing, and computing.
Novel tumor suppressor role of miRNA-876 in cholangiocarcinoma
Authors: Ursu Sarah , Majid Shahana , Garger Caroline , de Semir David , Bezrookove Vladimir , Desprez Pierre-Yves , McAllister Sean , Soroceanu Liliana , Nosrati Mehdi , Yimam Kidist , Hassoun Assad , Osorio Robert , Kashani-Sabet Mohammed , Dar Altaf A.
Published: August 2019

Cholangiocarcinoma (CCA) is a rare, highly invasive malignancy, and its incidence is increasing globally. MicroRNAs (miRNAs) mediate a wide array of cellular and biological processes and are dysregulated in various tumors. The functional and biological roles of miRNAs in CCA have not been fully elucidated. In this study, we show that miR-876 expression levels and copy number are significantly attenuated in the TCGA cohort of CCA tissue samples. TCGA expression data was consistent with the observed substantial decrease in miR-876 expression in patient samples and CCA cell lines. In-silico algorithm databases revealed BCL-XL as a potential target of miR-876. We observed miR-876 expression to be downregulated, whereas, BCL-XL upregulated in CCA cell lines. BCL-XL was identified as a direct functional target of miR-876 in CCA. miR-876-mediated reduction of BCL-XL regulated cell survival, induced apoptosis and caspase 3/7 expression in CCA. BCL-XL overexpression reversed the miR-876 mediated effect on CCA cell growth and apoptosis. Stable overexpression of miR-876 produced potent tumor suppressor activity and in vivo tumor cell growth reduction. Overexpression of miR-876 in a patient-derived xenograft (PDX) cell line significantly suppressed BCL-XL expression and spheroid formation with a concomitant induction of caspase 3/7 activity and apoptosis. This study demonstrates a novel tumor suppressor role for miR-876 in CCA, identifies BCL-XL as an actionable target, and suggests a potential therapeutic role for miR-876 in CCA.
mTOR direct crosstalk with STAT5 promotes de novo lipid synthesis and induces hepatocellular carcinoma
Authors: Li Ting , Weng Jun , Zhang Yue , Liang Kangyan , Fu Gongbo , Li Yang , Bai Xiaochun , Gao Yi
Published: August 2019

Hepatocellular carcinoma (HCC) can be the last step of nonalcoholic fatty liver disease (NAFLD) evolution, and the main characteristic of NAFLD is alteration in lipid metabolism. However, the mechanisms of abnormal lipid metabolism in NAFLD and HCC progression are yet to be identified. Here, we demonstrate that liver-specific activation of mTORC1 promoted the expression of lipid synthesis genes and lead to the development of spontaneous HCC. Genetic mouse models developed spontaneous HCC along with increased expressions of SREBP1, ACC1 and FASN. In addition, high levels of p-STAT5 were observed in the livers and particularly evident in the tumor area. And the synthesis of p-STAT5 was increased in patients along with the increase in SREBP1 synthesis in clinical samples. Moreover, mTORC1 interacts with and phosphorylates the STAT5 in hepatocytes. In conclusion, our data suggested that mTORC1 upregulates SREBP1 transcription via crosstalk with the STAT5 pathway which contributes to the NAFLD-related HCC pathogenesis. And the inhibitor of SREBP1 and mTOR may help to prevent HCC in clinical NAFLD patients.
Circular RNA PRKCI promotes glioma cell progression by inhibiting microRNA-545
Authors: Zhang Xuebang , Yang Han , Zhao Lihao , Li Gang , Duan Yuxia
Published: August 2019

We here tested expression and potential functions of circular RNA PRKCI (circPRKCI) in human glioma. Our results show that circPRKCI is upregulated in human glioma tissues and glioma cells, correlating with downregulation of its potential target, microRNA-545 (miR-545). In A172 and primary human glioma cells, shRNA-mediated silencing of circPRKCI inhibited cancer cell growth, survival, proliferation, and migration. Conversely, ectopic circPRKCI overexpression promoted A172 cell progression. miR-545 is the primary target of circPRKCI in glioma cells. Forced overexpression of miR-545 mimicked circPRKCI shRNA-induced actions, inhibiting glioma cell survival and proliferation. In contrast, miR-545 inhibition, by a lentiviral antagomiR-545 construct, reversed circPRKCI shRNA-induced anti-A172 cell activity. Importantly, neither circPRKCI shRNA nor circPRKCI overexpression was effective in miR-545-knockout (Cas9 method) A172 cells. Importantly, the subcutaneous and orthotopic A172 xenograft growth was significantly inhibited by circPRKCI silencing. Collectively, circPRKCI promotes human glioma cell progression possibly by inhibiting miR-545. Targeting circPRKCI-miR-545 cascade could efficiently inhibit human glioma cells.
Clinical characteristics with long-term follow-up of four Okinawan families with moderate hearing loss caused by an OTOG variant
Authors: Ganaha Akira , Kaname Tadashi , Yanagi Kumiko , Tono Tetsuya , Higa Teruyuki , Suzuki Mikio
Published: August 2019

We describe the clinical features of four Japanese families with moderate sensorineural hearing loss due to the OTOG gene variant. We analyzed 98 hearing loss-related genes in patients with hearing loss originally from the Okinawa Islands using next-generation sequencing. We identified a homozygous variant of the gene encoding otogelin NM_001277269(OTOG): c.330C>G, p.Tyr110* in four families. All patients had moderate hearing loss with a slightly downsloping audiogram, including low frequency hearing loss without equilibrium dysfunction. Progressive hearing loss was not observed over the long-term in any patient. Among the three patients who underwent newborn hearing screening, two patients passed the test. OTOG-associated hearing loss was considered to progress early after birth, leading to moderate hearing loss and the later stable phase of hearing loss. Therefore, there are patients whose hearing loss cannot be detected by NHS, making genetic diagnosis of OTOG variants highly useful for complementing NHS in the clinical setting. Based on the allele frequency results, hearing loss caused by the p.Tyr110* variant in OTOG might be more common than we identified. The p.Tyr110* variant was reported in South Korea, suggesting that this variant is a common cause of moderate hearing loss in Japanese and Korean populations.
Discrepancy in scientific authority and media visibility of climate change scientists and contrarians
Authors: Petersen Alexander Michael , Vincent Emmanuel M. , Westerling Anthony LeRoy
Published: August 2019

We juxtapose 386 prominent contrarians with 386 expert scientists by tracking their digital footprints across ∼200,000 research publications and ∼100,000 English-language digital and print media articles on climate change. Projecting these individuals across the same backdrop facilitates quantifying disparities in media visibility and scientific authority, and identifying organization patterns within their association networks. Here we show via direct comparison that contrarians are featured in 49% more media articles than scientists. Yet when comparing visibility in mainstream media sources only, we observe just a 1% excess visibility, which objectively demonstrates the crowding out of professional mainstream sources by the proliferation of new media sources, many of which contribute to the production and consumption of climate change disinformation at scale. These results demonstrate why climate scientists should increasingly exert their authority in scientific and public discourse, and why professional journalists and editors should adjust the disproportionate attention given to contrarians.
Visualization and design of the functional group distribution during statistical copolymerization
Authors: Van Steenberge Paul H. M. , Sedlacek Ondrej , Hernández-Ortiz Julio C. , Verbraeken Bart , Reyniers Marie-Françoise , Hoogenboom Richard , D’hooge Dagmar R.
Published: August 2019

Even though functional copolymers with a low percentage of functional comonomer units (up to 20 mol%) are widely used, for instance for the development of polymer therapeutics and hydrogels, insights in the functional group distribution over the actual chains are lacking and the average composition is conventionally used to describe the functionalization degree. Here we report the visualization of the monomer distribution over the different polymer chains by a synergetic combination of experimental and theoretical analysis aiming at the construction of functionality-chain length distributions (FUNC-CLDs). A successful design of the chemical structure of the comonomer pair, the initial functional comonomer amount (13 mol%), and the temperature (100 °C) is performed to tune the FUNC-CLD of copoly(2-oxazoline)s toward high functionalization degree for both low (100) and high (400) target degrees of polymerization. The proposed research strategy is generic and extendable to a broad range of copolymerization chemistries, including reversible deactivation radical polymerization.
Information-based centralization of locomotion in animals and robots
Authors: Neveln Izaak D. , Tirumalai Amoolya , Sponberg Simon
Published: August 2019

The centralization of locomotor control from weak and local coupling to strong and global is hard to assess outside of particular modeling frameworks. We developed an empirical, model-free measure of centralization that compares information between control signals and both global and local states. A second measure, co-information, quantifies the net redundancy in global and local control. We first validate that our measures predict centralization in simulations of phase-coupled oscillators. We then test how centralization changes with speed in freely running cockroaches. Surprisingly, across all speeds centralization is constant and muscle activity is more informative of the global kinematic state (the averages of all legs) than the local state of that muscle’s leg. Finally we use a legged robot to show that mechanical coupling alone can change the centralization of legged locomotion. The results of these systems span a design space of centralization and co-information for biological and robotic systems.
Bounded rationality in C. elegans is explained by circuit-specific normalization in chemosensory pathways
Authors: Cohen Dror , Teichman Guy , Volovich Meshi , Zeevi Yoav , Elbaum Lilach , Madar Asaf , Louie Kenway , Levy Dino J. , Rechavi Oded
Published: August 2019

Rational choice theory assumes optimality in decision-making. Violations of a basic axiom of economic rationality known as “Independence of Irrelevant Alternatives” (IIA) have been demonstrated in both humans and animals and could stem from common neuronal constraints. Here we develop tests for IIA in the nematode Caenorhabditis elegans, an animal with only 302 neurons, using olfactory chemotaxis assays. We find that in most cases C. elegans make rational decisions. However, by probing multiple neuronal architectures using various choice sets, we show that violations of rationality arise when the circuit of olfactory sensory neurons is asymmetric. We further show that genetic manipulations of the asymmetry between the AWC neurons can make the worm irrational. Last, a context-dependent normalization-based model of value coding and gain control explains how particular neuronal constraints on information coding give rise to irrationality. Thus, we demonstrate that bounded rationality could arise due to basic neuronal constraints.
Global Assessment of Retinal Arteriolar, Venular and Capillary Microcirculations Using Fundus Photographs and Optical Coherence Tomography Angiography in Diabetic Retinopathy
Authors: Tan Tien-En , Nguyen Quang , Chua Jacqueline , Schmetterer Leopold , Tan Gavin Siew Wei , Wong Chee Wai , Tsai Andrew , Cheung Gemmy Chui Ming , Wong Tien Yin , Ting Daniel Shu Wei
Published: August 2019

Retinal arterioles, venules and capillaries are differentially affected in diabetes, and studying vascular alterations may provide information on pathogenesis of diabetic retinopathy (DR). We conducted a cross-sectional study on 49 diabetic patients, who underwent fundus photography and optical coherence tomographic angiography (OCT-A). Fundus photographs were analysed using semi-automated software for arteriolar and venular parameters, including central retinal arteriolar equivalent (CRAE), central retinal venular equivalent (CRVE) and fractal dimension (FD). Capillary parameters were measured using OCT-A, including capillary density index (CDI) and capillary FD of superficial (SVP) and deep (DVP) vascular plexuses. Severe DR was defined as severe non-proliferative DR and proliferative DR. We found that eyes with severe DR had narrower CRAE and sparser SVP CDI than eyes without. In logistic regression analysis, capillary parameters were more associated with severe DR than arteriolar or venular parameters. However, combining arteriolar, venular and capillary parameters provided the strongest association with severe DR. In linear regression analysis, eyes with poorer visual acuity had lower CRAE and FD of arterioles, venules, and DVP capillaries. We concluded that the retinal microvasculature is globally affected in severe DR, reflecting widespread microvascular impairment in perfusion. Arteriolar, venular and capillary parameters provide complementary information in assessment of DR.
Airborne transmission may have played a role in the spread of 2015 highly pathogenic avian influenza outbreaks in the United States
Authors: Zhao Yang , Richardson Brad , Takle Eugene , Chai Lilong , Schmitt David , Xin Hongwei
Published: August 2019

The unprecedented 2015 outbreaks of highly pathogenic avian influenza (HPAI) H5N2 in the U.S. devastated its poultry industry and resulted in over $3 billion economic impacts. Today HPAI continues eroding poultry operations and disrupting animal protein supply chains around the world. Anecdotal evidence in 2015 suggested that in some cases the AI virus was aerially introduced into poultry houses, as abnormal bird mortality started near air inlets of the infected houses. This study modeled air movement trajectories and virus concentrations that were used to assess the probability or risk of airborne transmission for the 77 HPAI cases in Iowa. The results show that majority of the positive cases in Iowa might have received airborne virus, carried by fine particulate matter, from infected farms within the state (i.e., intrastate) and infected farms from the neighboring states (i.e., interstate). The modeled airborne virus concentrations at the Iowa recipient sites never exceeded the minimal infective doses for poultry; however, the continuous exposure might have increased airborne infection risks. In the worst-case scenario (i.e., maximum virus shedding rate, highest emission rate, and longest half-life), 33 Iowa cases had > 10% (three cases > 50%) infection probability, indicating a medium to high risk of airborne transmission for these cases. Probability of airborne HPAI infection could be affected by farm type, flock size, and distance to previously infected farms; and more importantly, it can be markedly reduced by swift depopulation and inlet air filtration. The research results provide insights into the risk of airborne transmission of HPAI virus via fine dust particles and the importance of preventative and containment strategies such as air filtration and quick depopulation of infected flocks.
Defining and detecting links in chromosomes
Authors: Niewieczerzal Szymon , Niemyska Wanda , Sulkowska Joanna I.
Published: August 2019

Sophisticated methods for mapping chromatin contacts enable to generate data of the genome structure that provide deep insights into the formation of chromatin interactions within cell nuclei. Due to the recent progress in this field, three-dimensional genomic structures of individual haploid mouse embryonic stem cells have been determined. Here, we analyze these data (8 cells) and determine comprehensive landscape of entanglements between interphase chromosomes. We find a significant number of stable links formed by chromosome pairs. Some links are even conserved between cells. Moreover, examples of stable multiple links, with at least three chromosomes engaged, are also identified. Types of links and their location along chromosomes are determined based on computations of HOMFLY-PT polynomials and Gauss Linking Numbers. Furthermore, stability of links is studied between different models, cells, and based on relaxation simulations of the genomic structure in a simplified structure-based representation. Identified links suggest that small fraction of chromosomes are entangled not only locally. How topoisomerases engineer such configurations remains an open question. Furthermore, presented methods can be used as a quantitative assessment – descriptor – to distinguish the quality of modeled data.
Establishment of serine protease htrA mutants in Helicobacter pylori is associated with secA mutations
Authors: Zawilak-Pawlik Anna , Zarzecka Urszula , Żyła-Uklejewicz Dorota , Lach Jakub , Strapagiel Dominik , Tegtmeyer Nicole , Böhm Manja , Backert Steffen , Skorko-Glonek Joanna
Published: August 2019

Helicobacter pylori plays an essential role in the pathogenesis of gastritis, peptic ulcer disease, and gastric cancer. The serine protease HtrA, an important secreted virulence factor, disrupts the gastric epithelium, which enables H. pylori to transmigrate across the epithelium and inject the oncogenic CagA protein into host cells. The function of periplasmic HtrA for the H. pylori cell is unknown, mainly due to unavailability of the htrA mutants. In fact, htrA has been described as an essential gene in this bacterium. We have screened 100 worldwide H. pylori isolates and show that only in the N6 strain it was possible to delete htrA or mutate the htrA gene to produce proteolytically inactive HtrA. We have sequenced the wild-type and mutant chromosomes and we found that inactivation of htrA is associated with mutations in SecA – a component of the Sec translocon apparatus used to translocate proteins from the cytoplasm into the periplasm. The cooperation of SecA and HtrA has been already suggested in Streptococcus pneumonia, in which these two proteins co-localize. Hence, our results pinpointing a potential functional relationship between HtrA and the Sec translocon in H. pylori possibly indicate for the more general mechanism responsible to maintain bacterial periplasmic homeostasis.
Amino acid supplementation of a simple inorganic salt solution supports efficient in vitro maturation (IVM) of bovine oocytes
Authors: Bahrami Mohammad , Morris Michael B. , Day Margot L.
Published: August 2019

Defining oocyte in vitro maturation (IVM) conditions allows for improved reproducibility and efficiency of bovine embryo production. IVM conditions for bovine oocytes have been extensively studied, but beneficial effects of individual supplements remain controversial. This study compared methods of cumulus oocyte complex (COC) isolation, and culture medium requirements, for IVM in order to define optimal conditions. Antral follicles in ovaries were sliced or aspirated to isolate COCs. Brilliant cresyl blue staining of COCs was used to determine the most effective collection technique and the effect of hormones and groups of amino acids in the culture medium was investigated. Our results showed COCs isolated through aspiration had greater meiotic competency to reach MII. Oocyte maturation was achieved with the addition of 1 µg/mL FSH, while estrogen and human chorionic gonadotrophin did not increase the number of MII oocytes. We also provide novel data, that supplementation of a simple inorganic salt solution with L-proline, L-glutamine and essential amino acids in combination, but not individually, resulted in nuclear maturation comparable to TCM199, a more complex medium containing all 20 common amino acids, vitamins, inorganic salts and FBS. Replacement of FBS with BSA in this simplified medium creates a defined medium which provides conditions for IVM that enable reproducible maturation rates.
Predicting seismic-induced liquefaction through ensemble learning frameworks
Authors: Alobaidi Mohammad H. , Meguid Mohamed A. , Chebana Fateh
Published: August 2019

The regional nature of liquefaction records and limited information available for a certain set of explanatories motivate the development of complex prediction techniques. Indirect methods are commonly applied to incidentally derive a hyperplane to this binary classification problem. Machine learning approaches offer evolutionary prediction models which can be used as direct prediction methods to liquefaction occurrence. Ensemble learning is a recent advancement in this field. According to a predefined ensemble architecture, a number of learners are trained and their inferences are integrated to produce stable and improved generalization ability. However, there is a need to consider several aspects of the ensemble learning frameworks when exploiting them for a particular application; a comprehensive evaluation of an ensemble learner’s generalization ability is required but usually overlooked. Also, the literature falls short on work utilizing ensemble learning in liquefaction prediction. To this extent, this work examines useful ensemble learning approaches for seismic-induced liquefaction prediction. A comprehensive analysis of fifteen ensemble models is performed. The results show improved prediction performance and diminishing uncertainty of ensembles, compared with single machine learning models.
Functional expression of CLIFAHDD and IHPRF pathogenic variants of the NALCN channel in neuronal cells reveals both gain- and loss-of-function properties
Authors: Bouasse Malik , Impheng Hathaichanok , Servant Zoe , Lory Philippe , Monteil Arnaud
Published: August 2019

The excitability of neurons is tightly dependent on their ion channel repertoire. Among these channels, the leak sodium channel NALCN plays a crucial role in the maintenance of the resting membrane potential. Importantly, NALCN mutations lead to complex neurodevelopmental syndromes, including infantile hypotonia with psychomotor retardation and characteristic facies (IHPRF) and congenital contractures of limbs and face, hypotonia and developmental delay (CLIFAHDD), which are recessively and dominantly inherited, respectively. Unfortunately, the biophysical properties of NALCN are still largely unknown to date, as well as the functional consequences of both IHPRF and CLIFAHDD mutations on NALCN current. Here we have set-up the heterologous expression of NALCN in the neuronal cell line NG108-15 to investigate the electrophysiological properties of NALCN carrying representative IHPRF and CLIFAHDD mutations. Several original properties of the wild-type (wt) NALCN current were retrieved: mainly carried by external Na+, blocked by Gd3+, insensitive to TTX and potentiated by low external Ca2+ concentration. However, we found that this current displays a time-dependent inactivation in the −80/−40 mV range of membrane potential, and a non linear current-voltage relationship indicative of voltage sensitivity. Importantly, no detectable current was recorded with the IHPRF missense mutation p.Trp1287Leu (W1287L), while the CLIFAHDD mutants, p.Leu509Ser (L509S) and p.Tyr578Ser (Y578S), showed higher current densities and slower inactivation, compared to wt NALCN current. This study reveals that heterologous expression of NALCN channel can be achieved in the neuronal cell line NG108-15 to study the electrophysiological properties of wt and mutants. From our results, we conclude that IHPRF and CLIFAHDD missense mutations are loss- and gain-of-function variants, respectively.
A novel nano-particle strengthened titanium alloy with exceptional specific strength
Authors: Dutt Aniket K. , Gwalani Bharat , Tungala Vedavyas , Carl Matthew , Mishra Rajiv S. , Tamirisakandala Sesh A. , Young Marcus L. , Cho Kyu C. , Brennan Raymond E.
Published: August 2019

Various ecological and economical concerns have spurred mankind’s quest for materials that can provide enhanced weight savings and improved fuel efficiency. As part of this pursuit, we have microstructurally tailored an exceptionally high-strength titanium alloy, Ti-6Al-2Sn-4Zr-6Mo (Ti6246) through friction stir processing (FSP). FSP has altered the as-received bimodal microstructure into a unique modulated microstructure comprised of fine acicular α″-laths with nano precipitates within the laths. The sequence of phase transformations responsible for the modulated microstructure and consequently for the strength is discussed with the help of scanning electron microscopy, transmission electron microscopy, and synchrotron X-ray diffraction studies. The specific strength attained in one of the conditions is close to 450 MPa m3/mg, which is about 22% to 85% greater than any commercially available metallic material. Therefore, our novel nano particle strengthened Ti alloy is a potential replacement for many structural alloys, enabling significant weight reduction opportunities.
A VNTR Regulates miR-137 Expression Through Novel Alternative Splicing and Contributes to Risk for Schizophrenia
Authors: Pacheco Ashley , Berger Ralph , Freedman Robert , Law Amanda J.
Published: August 2019

The MIR137HG gene encoding microRNA-137 (miR-137) is genome-wide associated with schizophrenia (SZ), however, the underlying molecular mechanisms remain unknown. Through cloning and sequencing of individual transcripts from fetal and adult human brain tissues we describe novel pri-miR-137 splice variants which exclude the mature miR-137 sequence termed ‘del-miR-137’ that would function to down-regulate miR-137 expression. Sequencing results demonstrate a significant positive association between del-miR-137 transcripts and the length of a proximal variable number tandem repeat (VNTR) element. Additionally, a significantly higher proportion of sequenced transcripts from fetal brain were del-miR-137 transcripts indicating neurodevelopmental splicing regulation. In-silico results predict an independent regulatory function for del-miR-137 transcripts through competitive endogenous RNA function. A case-control haplotype analysis (n = 998) in SZ implicates short VNTR length in risk, with longer lengths imparting a protective effect. Rare high risk haplotypes were also observed indicating multiple risk variants within the region. A second haplotype analysis was performed to evaluate recombination effects excluding the VNTR and results indicate that recombination of the region was found to independently contribute to risk. Evaluation of the evolutionary conservation of the VNTR reveals a human lineage specific expansion. These findings shed further light on the risk architecture of the miR-137 region and provide a novel regulatory mechanism through VNTR length and alternative MIR137HG transcripts which contribute to risk for SZ.
Survival-time dependent increase in neuronal IL-6 and astroglial GFAP expression in fatally injured human brain tissue
Authors: Trautz Florian , Franke Heike , Bohnert Simone , Hammer Niels , Müller Wolf , Stassart Ruth , Tse Rexson , Zwirner Johann , Dreßler Jan , Ondruschka Benjamin
Published: August 2019

Knowledge on trauma survival time prior to death following a lethal traumatic brain injury (TBI) may be essential for legal purposes. Immunohistochemistry studies might allow to narrow down this survival interval. The biomarkers interleukin-6 (IL-6) and glial fibrillary acidic protein (GFAP) are well known in the clinical setting for their usability in TBI prediction. Here, both proteins were chosen in forensics to determine whether neuronal or glial expression in various brain regions may be associated with the cause of death and the survival time prior to death following TBI. IL-6 positive neurons, glial cells and GFAP positive astrocytes all concordantly increase with longer trauma survival time, with statistically significant changes being evident from three days post-TBI (p < 0.05) in the pericontusional zone, irrespective of its definite cortical localization. IL-6 staining in neurons increases significantly in the cerebellum after trauma, whereas increasing GFAP positivity is also detected in the cortex contralateral to the focal lesion. These systematic chronological changes in biomarkers of pericontusional neurons and glial cells allow for an estimation of trauma survival time. Higher numbers of IL-6 and GFAP-stained cells above threshold values in the pericontusional zone substantiate the existence of fatal traumatic changes in the brain with reasonable certainty.
Assessing phenotype order in molecular data
Authors: Lausser Ludwig , Schäfer Lisa M. , Schirra Lyn-Rouven , Szekely Robin , Schmid Florian , Kestler Hans A.
Published: August 2019

Biological entities are key elements of biomedical research. Their definition and their relationships are important in areas such as phylogenetic reconstruction, developmental processes or tumor evolution. Hypotheses about relationships like phenotype order are often postulated based on prior knowledge or belief. Evidence on a molecular level is typically unknown and whether total orders are reflected in the molecular measurements is unclear or not assessed. In this work we propose a method that allows a fast and exhaustive screening for total orders in large datasets. We utilise ordinal classifier cascades to identify discriminable molecular representations of the phenotypes. These classifiers are constrained by an order hypothesis and are highly sensitive to incorrect assumptions. Two new error bounds, which are introduced and theoretically proven, lead to a substantial speed-up and allow the application to large collections of many phenotypes. In our experiments we show that by exhaustively evaluating all possible candidate orders, we are able to identify phenotype orders that best coincide with the high-dimensional molecular profiles.
The Thermomechanical Properties of Thermally Evaporated Bismuth Triiodide Thin Films
Authors: Coutinho Natália F. , Cucatti Silvia , Merlo Rafael B. , Silva Filho José Maria C. , Villegas Nelson F. Borrero , Alvarez Fernando , Nogueira Ana F. , Marques Francisco C.
Published: August 2019

Bismuth triiodide (BiI3) has been studied in recent years with the aim of developing lead-free semiconductors for photovoltaics. It has also appeared in X-ray detectors due to the high density of the Bismuth element. This material is attractive as an active layer in solar cells, or may be feasible for conversion into perovskite-like material (MA3Bi2I9), being also suitable for photovoltaic applications. In this study, we report on the thermomechanical properties (stress, hardness, coefficient of thermal expansion, and biaxial and reduced Young’s moduli) of BiI3 thin films deposited by thermal evaporation. The stress was determined as a function of temperature, adopting the thermally induced bending technique, which allowed us to extract the coefficient of thermal expansion (31 × 10−6 °C−1) and Young’s biaxial modulus (19.6 GPa) for the films. Nanohardness (~0.76 GPa) and a reduced Young’s modulus of 27.1 GPa were determined through nanoindentation measurements.