Miracle-dz/UniFAR-FTUs huggingface dataset:
SHIELD: an integrative gene expression database for inner ear research

The inner ear is a highly specialized mechanosensitive organ responsible for hearing and balance. Its small size and difficulty in harvesting sufficient tissue has hindered the progress of molecular studies. The protein components of mechanotransduction, the molecular biology of inner ear development and the genetic causes of many hereditary hearing and balance disorders remain largely unknown. Inner-ear gene expression data will help illuminate each of these areas. For over a decade, our laboratories and others have generated extensive sets of gene expression data for different cell types in the inner ear using various sample preparation methods and high-throughput genome-wide approaches. To facilitate the study of genes in the inner ear by efficient presentation of the accumulated data and to foster collaboration among investigators, we have developed the Shared Harvard Inner Ear Laboratory Database (SHIELD), an integrated resource that seeks to compile, organize and analyse the genomic, transcriptomic and proteomic knowledge of the inner ear. Five datasets are currently available. These datasets are combined in a relational database that integrates experimental data and annotations relevant to the inner ear. The SHIELD has a searchable web interface with two data retrieval options: viewing the gene pages online or downloading individual datasets as data tables. Each retrieved gene page shows the gene expression data and detailed gene information with hyperlinks to other online databases with up-to-date annotations. Downloadable data tables, for more convenient offline data analysis, are derived from publications and are current as of the time of publication. The SHIELD has made published and some unpublished data freely available to the public with the hope and expectation of accelerating discovery in the molecular biology of balance, hearing and deafness. Database URL: https://shield.hms. harvard.edu
Effects of Chemical, Organic and Bio-Fertilizers on Some Secondary Metabolites in the Leaves of Bell Pepper (Capsicum annuum) and Their Impact on Life Table Parameters of Myzus persicae (Hemiptera: Aphididae)

Abstract The green peach aphid, Myzus persicae (Sulzer), is a polyphagous and a holocyclic aphid that causes severe damage on hundreds of host plants in both fields and greenhouses. In this research, the effects of Zinc sulfate spray and amending the soil with 30% vermicompost, Bacillus subtilis, Pseudomonas fluorescens, Glomus intraradices, G. intraradices × B. subtilis, and G. intraradices × P. fluorescens compared with no fertilizer treatments were investigated on secondary metabolites in the leaves of bell pepper and life table parameters of M. persicae. Total phenol contents in the plant leaves varied significantly among different fertilizer treatments. The highest (72.28 mg/ml) value was observed on 30% vermicompost. Life table parameters of M. persicae were significantly affected by different fertilizer treatments. The net reproductive rate (R0) of M. persicae fed on plants treated with different fertilizer treatments varied from 4.38 to 21.93 female offspring, with the lowest and highest values on 30% vermicompost and Zinc sulfate, respectively. The lowest and the highest intrinsic rate of increase (rm) were also observed on 30% vermicompost and Zinc sulfate (0.111 and 0.321 female per female per day, respectively). The longest mean generation time (T) was recorded on 30% vermicompost (13.41 d), and the shortest generation time was observed on Zinc sulfate (9.61 d). Results of this study revealed that amending the soil with 30% vermicompost significantly affected the life table parameters of M. persicae. Thus, it was concluded that amending the soil of bell pepper with 30% vermicompost can provide an environmentally safe and efficient control of this aphid.
Effects of cage versus floor rearing environments and cage floor mesh size on bone strength, fearfulness, and production of single comb White Leghorn hens.

Fourteen hundred pullets were reared at densities of 304 and 735 cm2 in cages and floor pens with litter, respectively. Feeder spaces of 2.7, 4.0, and 5.4 cm per bird were held constant during the brooding growing period. At 18 wk of age, the birds were housed four birds per cage (348 cm2 per bird) in a force-ventilated, light-controlled house with two rows of stair-step cages. In two rows, the standard 2.5 x 5.0 cm welded wire flooring was replaced randomly with 2.5 x 2.5 cm welded wire in eight-cage sections. Egg production, egg quality, feed conversion, and mortality were measured over a 48-wk production cycle. At 68 wk of age, a sample of hens was selected and euthanatized, and the right leg was excised for further evaluation. Rearing environment, rearing feeder space, or type of layer floor mesh had no significant effects on hen-day production or feed conversion. Hens reared in cages produced heavier (P < .001) eggs with a higher percentage of Grade A eggs and had fewer body checks than floor-reared birds. Femur, tibia, and shank lengths were not affected by the rearing treatments or the type of flooring in the layer cage. Tibia breaking strength was not different for the rearing systems or hens maintained on 2.5 x 2.5 vs 2.5 x 5.0 cm welded wire mesh flooring. Hens reared in floor pens on litter displayed a higher level of fearfulness at the end of the production cycle. The reduced (P < .05) body weights associated with cage rearing and reduced feeder space did not negatively affect the production variables. Alteration of the mesh size of layer cage floor had no effect on the production levels of the hens.
Cardiometabolic Mortality by Supplemental Nutrition Assistance Program Participation and Eligibility in the United States

Objectives To investigate total and cause-specific cardiometabolic mortality among Supplemental Nutrition Assistance Program (SNAP) participants, SNAP-eligible nonparticipants, and SNAP-ineligible individuals overall and by age, gender, race/ethnicity, and other characteristics. Methods We performed a prospective study with nationally representative survey data from the National Health Interview Survey (2000-2009), merged with subsequent Public-Use Linked Mortality Files (2000-2011). We used survey-weighted Cox proportional hazards models adjusted for age and gender to estimate hazard ratios of total and cause-specific cardiometabolic mortality for 499 741 US adults aged 25 years or older. Results Over a mean of 6.8 years of follow-up (maximum 11.9 years), 39 293 deaths occurred, including 7408 heart disease, 2185 stroke, and 1376 diabetes deaths. Individuals participating in SNAP exhibited higher total and cardiovascular disease mortality, largely limited to non-Hispanic Whites and non-Hispanic Blacks, than both SNAP-eligible nonparticipants and SNAP-ineligible individuals, and higher diabetes mortality across races/ethnicities (P < .01). Conclusions Participants in SNAP require greater focus to understand and further address their poor health outcomes. Public Health Implications Low-income Americans require even greater efforts to improve their health than they currently receive, and such efforts should be a priority for public health policymakers.
The effect of iron-deficiency anaemia on two indices of nutritional status, prealbumin and transferrin

1. Serum prealbumin, transferrin and iron concentrations were measured in ninety-two north Cameroonian children under 5 years of age. The results were grouped according to the blood haemoglobin concentration range in order to show the interactions of anaemia with prealbumin and transferrin concentrations. 2. Transferrin concentration showed a significant negative correlation with serum Fe and percentage saturation of transferrin values. Prealbumin concentration showed a significant direct correlation with haemoglobin but did not correlate with either serum Fe or percentage saturation of transferrin. 3. It is concluded that in regions where Fe-deficiency anaemia is endemic transferrin concentration may be of little value in determining nutritional status. On the contrary, prealbumin seems to be more useful.
Nutritive value of high oil corn for poultry.

Several experiments were conducted to evaluate the nutritional value of high oil corn for poultry relative to that of conventional (CONV) corn. The variety of high oil corn (HO1) evaluated in most trials contained 6.0% oil and 9.6% protein on a 10% moisture basis. The protein quality of HO1 and CONV corn was assessed with female crossbred chicks fed corn as the sole source of dietary protein. There was no difference in either protein efficiency ratio or in net protein ratio between the two types of corn. True metabolizable energy (TME) and nitrogen-corrected TME (TMEn) values of HO1 corn were determined using adult roosters. The TME and TMEn values of HO1 corn were approximately 4.5% higher than those of CONV corn. Two experiments were conducted to evaluate the use of high oil corn varieties, containing from 6 to 13% oil, in practical diets of commercial broiler chicks from 8 to 22 days posthatching. Weight gain, gain-to-feed ratio, and skin and plasma pigmentation were improved in chicks fed 24% protein diets containing high oil corns compared with those fed the same diet containing CONV corn; magnitude of response was highly correlated to oil content of the corn. The relative value of HO1 corn in practical laying hen diets was examined in a 15-wk experiment. Hens fed a 17% protein diet containing HO1 corn from 23 to 38 weeks of age had a better feed-to-egg ratio than those fed the same diet containing CONV corn when the corn sources were substituted on an isonitrogenous basis. (ABSTRACT TRUNCATED AT 250 WORDS)
MaskGAN: Better Text Generation via Filling in the ______

Neural text generation models are often autoregressive language models or seq2seq models. These models generate text by sampling words sequentially, with each word conditioned on the previous word, and are state-of-the-art for several machine translation and summarization benchmarks. These benchmarks are often defined by validation perplexity even though this is not a direct measure of the quality of the generated text. Additionally, these models are typically trained via maxi- mum likelihood and teacher forcing. These methods are well-suited to optimizing perplexity but can result in poor sample quality since generating text requires conditioning on sequences of words that may have never been observed at training time. We propose to improve sample quality using Generative Adversarial Networks (GANs), which explicitly train the generator to produce high quality samples and have shown a lot of success in image generation. GANs were originally designed to output differentiable values, so discrete language generation is challenging for them. We claim that validation perplexity alone is not indicative of the quality of text generated by a model. We introduce an actor-critic conditional GAN that fills in missing text conditioned on the surrounding context. We show qualitatively and quantitatively, evidence that this produces more realistic conditional and unconditional text samples compared to a maximum likelihood trained model.
Goal-Oriented Chatbot Dialog Management Bootstrapping with Transfer Learning

Goal-Oriented (GO) Dialogue Systems, colloquially known as goal oriented chatbots, help users achieve a predefined goal (e.g. book a movie ticket) within a closed domain. A first step is to understand the user's goal by using natural language understanding techniques. Once the goal is known, the bot must manage a dialogue to achieve that goal, which is conducted with respect to a learnt policy. The success of the dialogue system depends on the quality of the policy, which is in turn reliant on the availability of high-quality training data for the policy learning method, for instance Deep Reinforcement Learning. Due to the domain specificity, the amount of available data is typically too low to allow the training of good dialogue policies. In this paper we introduce a transfer learning method to mitigate the effects of the low in-domain data availability. Our transfer learning based approach improves the bot's success rate by 20% in relative terms for distant domains and we more than double it for close domains, compared to the model without transfer learning. Moreover, the transfer learning chatbots learn the policy up to 5 to 10 times faster. Finally, as the transfer learning approach is complementary to additional processing such as warm-starting, we show that their joint application gives the best outcomes.
The upper critical ambient temperature in neonatal chicks.

Heat production, dry matter, and water loss in the body and yolk sac of neonatal broiler chicks were measured during 24 h exposure to constant temperatures from 30.8 to 38.8 C. Average initial body and yolk sac weights were 41.6 and 4.4 g, respectively. Chicks housed at 30.8 C lost 3.5 g/day and chicks housed at 38.8 C lost 5.7 g/day of total body weight. Between 30.8 and 35.1 C, weight loss of the yolk sac was 1.9 g/day. At 38.8 C, weight loss of the yolk sac was 1.4 g/day. Weight lost from the yolk sac consisted of equal amount of dry matter and water. Water loss from the remainder of the chick's body (the total body without yolk sac) increased from 1.8 to 4.4 g as environmental temperature was raised from 30.8 to 38.8 C. This increase occurred mainly above about 35 C. Chick heat production increased with ambient temperature. Heat production as determined per subsequent 3-h period decreased with increasing duration of exposure from 34.6 to 28.2 kJ/kg per hour (1 kJ = .239 kcal) at 30.8 C and from 44.1 to 35.5 kJ/kg per hour at 38.8 C. The upper critical temperature was derived from regression of heat production on temperature. Results showed that this critical temperature was between 36 and 37 C.
A Pragmatic Randomized Controlled Trial of 6-Step vs 3-Step Hand Hygiene Technique in Acute Hospital Care in the United Kingdom

OBJECTIVE To evaluate the microbiologic effectiveness of the World Health Organization’s 6-step and the Centers for Disease Control and Prevention’s 3-step hand hygiene techniques using alcohol-based handrub. DESIGN A parallel group randomized controlled trial. SETTING An acute care inner-city teaching hospital (Glasgow). PARTICIPANTS Doctors (n=42) and nurses (n=78) undertaking direct patient care. INTERVENTION Random 1:1 allocation of the 6-step (n=60) or the 3-step (n=60) technique. RESULTS The 6-step technique was microbiologically more effective at reducing the median log10 bacterial count. The 6-step technique reduced the count from 3.28 CFU/mL (95% CI, 3.11–3.38 CFU/mL) to 2.58 CFU/mL (2.08–2.93 CFU/mL), whereas the 3-step reduced it from 3.08 CFU/mL (2.977–3.27 CFU/mL) to 2.88 CFU/mL (−2.58 to 3.15 CFU/mL) (P=.02). However, the 6-step technique did not increase the total hand coverage area (98.8% vs 99.0%, P=.15) and required 15% (95% CI, 6%-24%) more time (42.50 seconds vs 35.0 seconds, P=.002). Total hand coverage was not related to the reduction in bacterial count. CONCLUSIONS Two techniques for hand hygiene using alcohol-based handrub are promoted in international guidance, the 6-step by the World Health Organization and 3-step by the Centers for Disease Control and Prevention. The study provides the first evidence in a randomized controlled trial that the 6-step technique is superior, thus these international guidance documents should consider this evidence, as should healthcare organizations using the 3-step technique in practice. Infect Control Hosp Epidemiol 2016;37:661–666
Factors associated with relapse in schizophrenia despite adherence to long-acting injectable antipsychotic therapy

Many patients with schizophrenia will relapse despite uninterrupted antipsychotic (AP) long-acting therapy (LAT). This exploratory analysis examined variables associated with relapse despite ensured adherence to LAT. This was a post-hoc exploratory analysis of a 1-year study of risperidone long-acting injection in patients with stable schizophrenia or schizoaffective disorder (NCT00297388; N=323). Patients were discontinued from previous oral APs and randomly assigned to biweekly intramuscular injections of risperidone long-acting injectable 50 (n=163) or 25 mg (n=161) for 52 weeks. Cox proportional hazards regression models examined variables putatively associated with relapse. A total of 59/323 (18.3%) patients relapsed over 12 months despite continuous AP LAT. Variables associated with the risk of relapse included illness duration (6.0% increase each year; P=0.0003) and country (Canada vs. USA, 4.7-fold risk increase; P=0.0008). When illness duration was further categorized as ⩽5, 6–10, and >10 years, patients with an illness duration of >10 versus ⩽5 years were at greatest risk of relapse (>10 vs. ⩽5 years associated with a 4.4-fold increase in the risk of relapse; P=0.0181). Findings suggest that patients with more chronic illness have a greater risk of relapse despite ensured treatment adherence, supporting the need for early intervention to prevent the deleterious effects of chronicity.
Thermal Bimorph Micro-Cantilever Based Nano-Calorimeter for Sensing of Energetic Materials

Thermal Bimorph Micro-Cantilever Based Nano-Calorimeter for Sensing of Energetic Materials. (May 2012) Seokwon Kang, B.S., Hanyang University; M.S., Korea Advanced Institute of Science and Technology (KAIST) Chair of Advisory Committee: Dr. Debjyoti Banerjee The objective of this study is to develop a robust portable nano-calorimeter sensor for detection of energetic materials, primarily explosives, combustible materials and propellants. A micro-cantilever sensor array is actuated thermally using bi-morph structure consisting of gold (Au: 400 nm) and silicon nitride (Si3N4: 600 nm) thin film layers of sub-micron thickness. An array of micro-heaters is integrated with the microcantilevers at their base. On electrically activating the micro-heaters at different actuation currents the microcantilevers undergo thermo-mechanical deformation, due to differential coefficient of thermal expansion. This deformation is tracked by monitoring the reflected ray from a laser illuminating the individual microcantilevers (i.e., using the optical lever principle). In the presence of explosive vapors, the change in bending response of microcantilever is affected by the induced thermal stresses arising from temperature changes due to adsorption and combustion reactions (catalyzed by the gold surface). A parametric study was performed for investigating the optimum values by varying the thickness and length in parallel with the heater power since the sensor
Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y2 Receptor

Understanding the agonist-receptor interactions in the neuropeptide Y (NPY)/peptide YY (PYY) signaling system is fundamental for the design of novel modulators of appetite regulation. We report here the results of a multidisciplinary approach to elucidate the binding mode of the native peptide agonist PYY to the human Y2 receptor, based on computational modeling, peptide chemistry and in vitro pharmacological analyses. The preserved binding orientation proposed for full-length PYY and five analogs, truncated at the amino terminus, explains our pharmacological results where truncations of the N-terminal proline helix showed little effect on peptide affinity. This was followed by receptor mutagenesis to investigate the roles of several receptor positions suggested by the modeling. As a complement, PYY-(3-36) analogs were synthesized with modifications at different positions in the common PYY/NPY C-terminal fragment (32TRQRY36-amide). The results were assessed and interpreted by molecular dynamics and Free Energy Perturbation (FEP) simulations of selected mutants, providing a detailed map of the interactions of the PYY/NPY C-terminal fragment with the transmembrane cavity of the Y2 receptor. The amidated C-terminus would be stabilized by polar interactions with Gln2886.55 and Tyr2195.39, while Gln1303.32 contributes to interactions with Q34 in the peptide and T32 is close to the tip of TM7 in the receptor. This leaves the core, α-helix of the peptide exposed to make potential interactions with the extracellular loops. This model agrees with most experimental data available for the Y2 system and can be used as a basis for optimization of Y2 receptor agonists.
The NLR family pyrin domain–containing 11 protein contributes to the regulation of inflammatory signaling

Mammalian Nod-like receptor (NLR) proteins contribute to the regulation and induction of innate and adaptive immunity in mammals, although the function of about half of the currently identified NLR proteins remains poorly characterized. Here we analyzed the function of the primate-specific NLRP11 gene product. We show that NLRP11 is highly expressed in immune cells, including myeloid cells, B cells, and some B cell lymphoma lines. Overexpression of NLRP11 in human cells did not trigger key innate immune signaling pathways, including NF-κB and type I interferon responses. NLRP11 harbors a pyrin domain, which is responsible for inflammasome formation in related NLR proteins. However, NLRP11 did not interact with the inflammasome adaptor protein ASC, and it did not trigger caspase-1 activation. By contrast, expression of NLRP11 specifically repressed NF-κB and type I interferon responses, two key innate immune pathways involved in inflammation. This effect was independent of the pyrin domain and ATPase activity of NLRP11. siRNA-mediated knockdown of NLRP11 in human myeloid THP1 cells validated these findings and revealed enhanced lipopolysaccharide and Sendai virus–induced cytokine and interferon responses, respectively, in cells with reduced NLRP11 expression. In summary, our work identifies a novel role of NLRP11 in the regulation of inflammatory responses in human cells.
Regulation of Stomatal Immunity by Interdependent Functions of a Pathogen-Responsive MPK3/MPK6 Cascade and Abscisic Acid

MPK3/MPK6 cascade and ABA function interdependently to regulate stomatal immunity by modulating the organic acid metabolism and ion channels, respectively. Activation of mitogen-activated protein kinases (MAPKs) is one of the earliest responses after plants sense an invading pathogen. Here, we show that MPK3 and MPK6, two Arabidopsis thaliana pathogen-responsive MAPKs, and their upstream MAPK kinases, MKK4 and MKK5, are essential to both stomatal and apoplastic immunity. Loss of function of MPK3 and MPK6, or their upstream MKK4 and MKK5, abolishes pathogen/microbe-associated molecular pattern- and pathogen-induced stomatal closure. Gain-of-function activation of MPK3/MPK6 induces stomatal closure independently of abscisic acid (ABA) biosynthesis and signaling. In contrast, exogenously applied organic acids such as malate or citrate are able to reverse the stomatal closure induced by MPK3/MPK6 activation. Gene expression analysis and in situ enzyme activity staining revealed that malate metabolism increases in guard cells after activation of MPK3/MPK6 or inoculation of pathogen. In addition, pathogen-induced malate metabolism requires functional MKK4/MKK5 and MPK3/MPK6. We propose that the pathogen-responsive MPK3/MPK6 cascade and ABA are two essential signaling pathways that control, respectively, the organic acid metabolism and ion channels, two main branches of osmotic regulation in guard cells that function interdependently to control stomatal opening/closure.