Miracle-dz/UniFAR-FTUs huggingface dataset:
Tree-Structured Composition in Neural Networks without Tree-Structured Architectures

Tree-structured neural networks encode a particular tree geometry for a sentence in the network design. However, these models have at best only slightly outperformed simpler sequence-based models. We hypothesize that neural sequence models like LSTMs are in fact able to discover and implicitly use recursive compositional structure, at least for tasks with clear cues to that structure in the data. We demonstrate this possibility using an artificial data task for which recursive compositional structure is crucial, and find an LSTM-based sequence model can indeed learn to exploit the underlying tree structure. However, its performance consistently lags behind that of tree models, even on large training sets, suggesting that tree-structured models are more effective at exploiting recursive structure.
Salivary Biomarkers for Detection of Oral Squamous Cell Carcinoma in a Taiwanese Population

Purpose: This study evaluated the discriminatory power of salivary transcriptomic and proteomic biomarkers in distinguishing oral squamous cell carcinoma cases from controls and potentially malignant oral disorders (PMOD). Experimental Design: A total of 180 samples (60 OSCC patients, 60 controls, and 60 PMOD patients) were used in the study. Seven transcriptomic markers (IL8, IL1β, SAT1, OAZ1, DUSP1, S100P, and H3F3A) were measured using qPCR, and two proteomic markers (IL8 and IL1β) were evaluated by ELISA. Results: Among 7 transcriptomic markers, transcript level of DUSP1 was significantly lower in OSCC patients than in controls and PMOD patients. Between the proteomic markers, the protein concentration of IL8 and IL1β was significantly higher in OSCC patients than controls and dysplasia patients. Univariate fractional polynomial (FP) models revealed that salivary IL8 protein (IL8p) has the highest AUC value between OSCC patients and controls (0.74) and between OSCC and PMOD patients (0.72). Applying a 2-marker FP model, salivary IL8p combined with IL1β gave the best AUC value for discrimination between OSCC patients and controls, as well as the IL8p combined with H3F3A mRNA, which gave the best AUC value for discrimination between OSCC and PMOD patients. Multivariate models analysis combining salivary analytes and risk factor exposure related to oral carcinogenesis formed the best combinatory variables for differentiation between OSCC versus PMOL (AUC = 0.80), OSCC versus controls (AUC = 0.87), and PMOD versus controls (AUC = 0.78). Conclusions: The combination of transcriptomic and proteomic salivary markers is of great value for oral cancer detection and differentiation from PMOD patients and controls. Clin Cancer Res; 22(13); 3340–7. ©2016 AACR.
Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density

MicroRNAs (miRNAs) are post-transcriptional regulators that bind to their target mRNAs through base complementarity. Predicting miRNA targets is a challenging task and various studies showed that existing algorithms suffer from high number of false predictions and low to moderate overlap in their predictions. Until recently, very few algorithms considered the dynamic nature of the interactions, including the effect of less specific interactions, the miRNA expression level, and the effect of combinatorial miRNA binding. Addressing these issues can result in a more accurate miRNA:mRNA modeling with many applications, including efficient miRNA-related SNP evaluation. We present a novel thermodynamic model based on the Fermi-Dirac equation that incorporates miRNA expression in the prediction of target occupancy and we show that it improves the performance of two popular single miRNA target finders. Modeling combinatorial miRNA targeting is a natural extension of this model. Two other algorithms show improved prediction efficiency when combinatorial binding models were considered. ComiR (Combinatorial miRNA targeting), a novel algorithm we developed, incorporates the improved predictions of the four target finders into a single probabilistic score using ensemble learning. Combining target scores of multiple miRNAs using ComiR improves predictions over the naïve method for target combination. ComiR scoring scheme can be used for identification of SNPs affecting miRNA binding. As proof of principle, ComiR identified rs17737058 as disruptive to the miR-488-5p:NCOA1 interaction, which we confirmed in vitro. We also found rs17737058 to be significantly associated with decreased bone mineral density (BMD) in two independent cohorts indicating that the miR-488-5p/NCOA1 regulatory axis is likely critical in maintaining BMD in women. With increasing availability of comprehensive high-throughput datasets from patients ComiR is expected to become an essential tool for miRNA-related studies.
SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans

Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of melanocytes. Here we show that zebrafish golden mutants share these melanosomal changes and that golden encodes a putative cation exchanger slc24a5 (nckx5) that localizes to an intracellular membrane, likely the melanosome or its precursor. The human ortholog is highly similar in sequence and functional in zebrafish. The evolutionarily conserved ancestral allele of a human coding polymorphism predominates in African and East Asian populations. In contrast, the variant allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation.
Effect of ENEPIG Surface Finish on the Vibration Reliability of Solder Interconnects

Surface finishes are used to preserve and promote solderability of exposed copper metallization on printed wiring boards. While in the best of worlds, the solder used in assembly should dictate the solder interconnect reliability, surface finishes are known to have an effect. The effect of surface finishes on solder interconnect reliability can be particularly strong under high strain rate loading conditions. In this study, durability of solder interconnects formed between BGAs and electroless nickel, electroless palladium, immersion gold (ENEPIG) finished pads assembled using SnPb and SAC305 solders under harmonic vibration loading is examined. ENEPIG test specimens with two thicknesses of palladium were evaluated. Isothermal preconditioning levels at 100°C for 24 hrs and 500 hrs were included to evaluate the impact of intermetalic evolution on the durability of the soldered interconnects. For comparison, tests specimens created with immersion silver (ImAg) finished printed wiring boards were also includ.
Lack of Association of Interferon Regulatory Factor 1 with Severe Malaria in Affected Child-Parental Trio Studies across Three African Populations

Interferon Regulatory Factor 1 (IRF-1) is a member of the IRF family of transcription factors, which have key and diverse roles in the gene-regulatory networks of the immune system. IRF-1 has been described as a critical mediator of IFN-gamma signalling and as the major player in driving TH1 type responses. It is therefore likely to be crucial in both innate and adaptive responses against intracellular pathogens such as Plasmodium falciparum. Polymorphisms at the human IRF1 locus have been previously found to be associated with the ability to control P. falciparum infection in populations naturally exposed to malaria. In order to test whether genetic variation at the IRF1 locus also affects the risk of developing severe malaria, we performed a family-based test of association for 18 Single Nucleotide Polymorphisms (SNPs) across the gene in three African populations, using genotype data from 961 trios consisting of one affected child and his/her two parents (555 from The Gambia, 204 from Kenya and 202 from Malawi). No significant association with severe malaria or severe malaria subphenotypes (cerebral malaria and severe malaria anaemia) was observed for any of the SNPs/haplotypes tested in any of the study populations. Our results offer no evidence that the molecular pathways regulated by the transcription factor IRF-1 are involved in the immune-based pathogenesis of severe malaria.
A Deep-Learning-Based Method of Estimating Water Intake

In Japan, which has become a very aged society, the increasing burden of nursing care is an issue. Services and systems related to automatic recording of healthcare management of elderly people have been proposed in order to reduce the burden of nursing care. Water intake is one of the items necessary for healthcare management of elderly people. However, it is not currently automated, which is a burden on caregivers. In the case of the conventional method, the swallowing sound is used for estimating the water intake. However, the estimation error for each subject is large. Accuracy of estimated water intake is improved by using deep learning. Specifically, three features, namely, mel frequency cepstral coefficient (MFCC), duration of water intake, and a RASTA filter auditory spectrum, are extracted from a subject's swallowing sound (which is thought to be highly correlated with water intake). A method of estimating water intake, which considers abstract features that are difficult for people to find, is proposed and verified. It is experimentally shown that RMSE of water intake estimated by the proposed method using deep learning is reduced compared with that estimated by conventional methods.
Psychiatric Comorbidity, Sexual Dysfunction, and Quality of Life in Patients Undergoing Hemodialysis: A Case-Control Study.

INTRODUCTION Due to disabilities caused by the disease and the requirement of dialysis, end-stage renal disease (ESRD) is frequently comorbid with psychiatric disorders, adversely affects quality of life, and causes significant sexual dysfunction (SD). We aimed to investigate the psychiatric comorbidity, quality of life, depression and anxiety levels, and SD in ESRD patients undergoing hemodialysis. METHODS Forty-nine patients undergoing hemodialysis treatment in a dialysis center and 44 non-ESRD control subjects selected with snowball sampling were enrolled in the study. All subjects were assessed using Structured Clinical Interview for Axis-I Disorders (SCID-I). Sociodemographic data form, Hospital Anxiety and Depression Scale (HADS), Arizona Sexual Experience Scale (ASEX), and World Health Organization Quality of Life Short Form Turkish Version Scale (WHOQOL-BREF-TR) were applied to both groups. RESULTS There was no difference between the groups in terms of sex, age, education period, marital status, presence of additional physical illness, and past history of psychiatric disorders. Compared with the control group, HADS depression subscale and ASEX scores were significantly high (p<0.01) in the patient group, and WHOQOL-BREF-TR psychological and physical domain scores were low (p<0.05 and p<0.01, respectively). There was a significant negative relationship between HADS scores and WHOQOL-BREF-TR psychological, environmental, and national environmental scores in the patient group (p<0.05). When the differences between the groups were re-analyzed after controlling HADS depression scores with covariance analysis, the significant difference in ASEX and WHOQOL-BREF-TR physical domain scores between the groups remained, but the significant difference in WHOQOL-BREF-TR psychological domain scores disappeared. CONCLUSION The quality of life of ESRD patients was lower, especially in the psychological and physical domains, and psychiatric comorbidities and SD rates were higher than in non-ESRD control subjects. Quality of life is affected by SD. Recognizing and treating depressive symptoms will help improve the quality of life, especially in the psychological domain.
Low activity of select Hsp104 mutants is sufficient to propagate unstable prion variants

The molecular chaperone network plays a critical role in the formation and propagation of self-replicating yeast prions. Not only do individual prions differ in their requirements for certain chaperones, but structural variants of the same prion can also display distinct dependences on the chaperone machinery, specifically Hsp104. The AAA+ ATPase Hsp104 is a disaggregase required for the maintenance of most known yeast prions. As a key component in the propagation of prions, understanding how Hsp104 differs in its interaction with specific variants is crucial to understanding how prion variants may be selected or evolve. Here, we investigate two novel mutations in Hsp104, hsp104-G254D, and hsp104-G730D, which allow us to elucidate some mechanistic features of Hsp104 disaggregation and its requirement for activity in propagating specific prion variants. Both Hsp104 mutants propagate the [PSI+] prion to some extent, but show a high rate of prion loss. Both Hsp104-G254D and Hsp104-G730D display reduced biochemical activity, yet differ in their ability to efficiently resolubilize disordered, heat-aggregated substrates. Additionally, both mutants impair weak [PSI+] propagation, but are capable of propagating the less stable strong [PSI+] variant to some extent. One of the Hsp104 mutants also has the ability to propagate one variant of the [RNQ+] prion. Thus, our data suggest that changes in Hsp104 activity limit substrate disaggregation in a manner that depends more on the stability of the substrate than the nature of the aggregated species.
A Bead-Based Multiplexed Immunoassay to Evaluate Breast Cancer Biomarkers for Early Detection in Pre-Diagnostic Serum

This study investigates whether a set of ten potential breast cancer serum biomarkers and cancer antigens (osteopontin (OPN), haptoglobin, cancer antigen 15-3 (CA15-3), carcinoembryonic antigen (CEA), cancer antigen 125 (CA-125), prolactin, cancer antigen 19-9 (CA19-9), α-fetoprotein (AFP), leptin and migration inhibitory factor (MIF)) can predict early stage breast cancer in samples collected before clinical diagnosis (phase III samples). We performed a nested case-control study within the Prospect-EPIC (European Prospective Investigation into Cancer and nutrition) cohort. We examined to what extent the biomarker panel could discriminate between 68 women diagnosed with breast cancer up to three years after enrollment and 68 matched healthy controls (all 56–64 years at baseline). Using a quantitative bead-based multiplexed assay, we determined protein concentrations in serum samples collected at enrollment. Principal Component Analysis (PCA) and Random Forest (RF) analysis revealed that on the basis of all ten proteins, early cases could not be separated from controls. When we combined serum protein concentrations and subject characteristics related to breast cancer risk in the RF analysis, this did not result in classification accuracy scores that could correctly classify the samples (sensitivity: 50%, specificity: 50%). Our findings indicate that this panel of selected tumor markers cannot be used for diagnosis of early breast cancer.
Morphogen-based simulation model of ray growth and joint patterning during fin development and regeneration

The fact that some organisms are able to regenerate organs of the correct shape and size following amputation is particularly fascinating, but the mechanism by which this occurs remains poorly understood. The zebrafish (Danio rerio) caudal fin has emerged as a model system for the study of bone development and regeneration. The fin comprises 16 to 18 bony rays, each containing multiple joints along its proximodistal axis that give rise to segments. Experimental observations on fin ray growth, regeneration and joint formation have been described, but no unified theory has yet been put forward to explain how growth and joint patterns are controlled. We present a model for the control of fin ray growth during development and regeneration, integrated with a model for joint pattern formation, which is in agreement with published, as well as new, experimental data. We propose that fin ray growth and joint patterning are coordinated through the interaction of three morphogens. When the model is extended to incorporate multiple rays across the fin, it also accounts for how the caudal fin acquires its shape during development, and regains its correct size and shape following amputation.
Differences in adaptations to 1 year of aerobic endurance training: individual patterns of nonresponse

Lacking responses to endurance training (ET) have been observed for several variables. However, detailed analyses of individuals' responses are scarce. To learn more about the variability of ET adaptations, patterns of response were analyzed for each subject in a 1‐year ET study. Eighteen participants [42±5 years, body mass index: 24±3 kg/m2, maximal oxygen uptake (VO2max): 38±5 mL/min/kg] completed a 1‐year jogging/walking program on 3 days/week, 45 min/session at 60% heart rate (HR) reserve. VO2max, resting HR (rHR), exercise HR (eHR) and individual anaerobic threshold (IAT) were determined by treadmill and cycling ergometry respectively. Intraindividual coefficients of variation were extracted from the literature to distinguish random changes from training responses. Eight participants showed improvements in all variables. In 10 participants, one or two variables did not improve (VO2max, rHR, eHR and IAT remained unchanged in four, four, three and one cases, respectively). At least one variable improved in each subject. Data indicate that ET adaptations might be detected in each individual using multiple variables of different adaptation levels and intensity domains. Nonresponse seems to occur frequently and might affect all variables. Further studies should investigate whether nonresponders improve with altered training. Furthermore, associations between patterns of nonresponse and health benefits from ET are worth considering.
Oviposition Deterrence and Immature Survival of Filth Flies (Diptera: Muscidae) When Exposed to Commercial Fungal Products

Filth flies are pests of livestock, and can transmit pathogens that cause disease to animals and their caretakers. Studies have shown successful infection of adult filth flies following exposure to different strains and formulations of entomopathogenic fungi. This study aimed to examine the effects of commercial formulations of Beauveria bassiana (Balsamo) (Moniliales: Moniliaceae) (i.e., BotaniGard ES, Mycotrol O, balEnce), and Metarhizium brunneum (Metsch.) (Ascomycota: Hypocreales) (i.e., Met52 EC), on filth fly oviposition and immature fly survival after exposure. House flies, Musca domestica L. , laid significantly fewer eggs on Met52 EC-treated surfaces than on surfaces treated with all other products and the control. Similar numbers of eggs were laid on surfaces treated with all B. bassiana products, but egg production was half of the control. Stable flies, Stomoxys calcitrans (L.), laid the fewest eggs on Met52 EC- and Mycotrol O-treated surfaces. This species did not distinguish between the remaining products and the control. In a second experiment, house fly eggs were placed on treated cloths so that hatched larvae contacted the treatment prior to development. Met52 EC had the greatest effect on immature survival with a significant reduction in recovered pupae at the medium and high doses of fungi. Overall, Met52 EC, containing M. brunneum, had the greatest effect on house fly and stable fly oviposition deterrence and immature development of house flies. Management implications are discussed.
Sequences from the First Fibronectin Type III Repeat of the Neural Cell Adhesion Molecule Allow O-Glycan Polysialylation of an Adhesion Molecule Chimera*

Polysialic acid is a developmentally regulated, anti-adhesive polymer that is added to N-glycans on the fifth immunoglobulin domain (Ig5) of the neural cell adhesion molecule (NCAM). We found that the first fibronectin type III repeat (FN1) of NCAM is required for the polysialylation of N-glycans on the adjacent Ig5 domain, and we proposed that the polysialyltransferases recognize specific sequences in FN1 to position themselves for Ig5 N-glycan polysialylation. Other studies identified a novel FN1 acidic surface patch and α-helix that play roles in NCAM polysialylation. Here, we characterize the contribution of two additional FN1 sequences, Pro510-Tyr511-Ser512 (PYS) and Gln516-Val517-Gln518 (QVQ). Replacing PYS or the acidic patch dramatically decreases the O-glycan polysialylation of a truncated NCAM protein, and replacing the α-helix or QVQ shifts polysialic acid to FN1 O-glycans in full-length NCAM. We also found that the FN1 domain of the olfactory cell adhesion molecule, a homologous but unpolysialylated protein, could partially replace NCAM FN1. Inserting Pro510-Tyr511 eliminated N-glycan polysialylation and enhanced O-glycosylation of an NCAM- olfactory cell adhesion molecule chimera, and inserting other FN1 sequences unique to NCAM, predominantly the acidic patch, created a new polysialyltransferase recognition site. Taken together, our results highlight the role of the FN1 α-helix and QVQ sequences in N-glycan polysialylation and demonstrate that the acidic patch primarily functions in O-glycan polysialylation.
Highly Elastic Strain Gauges Based on Shape Memory Alloys for Monitoring of Fibre Reinforced Plastics

Conventional strain gauges made of constantan or CuCr for instance have a low value for structural health monitoring issues in plastic composites. These strain sensor materials exhibit small elastic regions and show fatigue when dynamically loaded with strain levels over 0.3 percent. For this reason, these sensors would break or fail before the composite life-time and thus cannot be integrated into this kind of composite materials. Pseudoelastic thermal shape memory alloys are therefore used as strain sensors and integrated into composites in order to allow piezoresistive strain measurement and structural health monitoring in such materials. Thermal treatments are used to create sensor structures out of shape memory alloy wires. Pseudoelastic shape memory wires can be strained up to 8 percent repeatedly. Their gauge factor is higher than 5. Shape memory strain sensors are successfully embedded into glass fibre reinforced plastics and show a significant and reproducible resistance change when the composite is strained. The dynamic strength is magnificently higher compared to conventional strain gauges. Shape memory strain sensors are an efficient alternative to fiber-bragg-grating sensors and can potentially be used for strain measurements in different plastics and textile materials. Shape memory sensor structures can be embedded or applied and are good candidates for structural characterisation and monitoring applications.
Comparison of Masculine and Feminine Traits in a National Sample of Male and Female Nursing Students

The stereotype that male nurses are less masculine has existed for generations and spans all age groups. Several studies have investigated masculinity and femininity in nurses using the Bem Sex-Role Inventory, but the results are conflicting and inconclusive. Therefore, a nationwide survey was conducted across the United States that examined the sex-role identity of individuals who chose nursing as a career path. Twenty-eight males and 81 females from 37 states completed the survey. The males and females in the study both had higher mean scores on masculinity and femininity scales when compared with previous studies. The greatest percentage of participants were classified as androgynous, as opposed to masculine, feminine, or undifferentiated, with half of the males and nearly half of the females falling into this category.