Miracle-dz/UniFAR-FTUs huggingface dataset:
Skin-core morphology and humidity effects on the fatigue crack propagation of PA-6.6

Effect of the skin and core morphology on the fatigue crack propagation behaviour was studied in injection-moulded polyamide 6.6 specimens in both the as-received dry state and a water-saturated, wet state. The morphology was visualised by polarised light micrographs which revealed a band structure in the specimens
Profile of disabilities and their associated factors in patients with type 2 diabetes evaluated by the Canadian occupational performance measure: the Rio De Janeiro type 2 diabetes cohort study

Abstract Purpose: To investigate the profile of disability in patients with type 2 diabetes and to evaluate its associated variables. Method: The Canadian Occupational Performance Measure (COPM) assessed disabilities in 475 type 2 diabetic individuals. The activities were categorised by the International Classification of Functioning, Disability and Health. The Medical Outcomes Study 36-item Short-Form Health Survey (SF-36) was used to evaluate pain, emotional and physical functioning domains of life-quality. Multivariable logistic regression assessed the independent correlates of better/worse performance. Results:: Median COPM score was 4.5 (interquartile range 3–6). Problems in mobility (53.6%), self-care (21.1%) and daily-life (13.0%) were most frequently self-reported. Presence of restriction/pain in the upper limbs (odds ratio [OR]: 1.66; 95% CI: 1.11–2.47; p=0.013) and of peripheral neuropathy (OR: 1.64; 95% CI: 1.06–2.53; p=0.026) were associated with greater chance of worse performance. Higher values of SF-36 in pain and emotional domains (each 10 point increase; OR: 0.92 95% CI: 0.85–0.98; p=0.011; OR: 0.96; 95% CI: 0.92–1.00; p=0.063, respectively) and physical activity (OR: 0.63; 95% CI: 0.41–0.98; p=0.042) were associated with better performance. Conclusions:: Type 2 diabetic patients frequently reported disabilities in mobility, self-care and daily-life domains; and its associated factors were the presence of depression, upper limb pain and diabetic peripheral neuropathy. Implications for Rehabilitation The Canadian Occupational Performance Measure (COPM) instrument can be applied to patients with diabetes, as it identifies several disabilities, mostly in mobility, self-care and domestic life areas. Rehabilitation directed to upper limb pain/limitation and to lower limb peripheral neuropathy shall be implemented and may improve diabetic patients’ performance and quality of life. A patient-centered rehabilitation strategy, guided by the COPM, may enable greater independence and autonomy, but this should be confirmed in future intervention studies.
Operations Research (OR)

400 Level Courses OR 438: Analytics for Financial Engineering and Econometrics. 3 credits. Introduces the basic analytics for financial engineering and econometrics. Topics include financial transactions and econometric data management, correlation, linear and multiple regressions for financial and economic predictions, financial time series analysis, portfolio theory, and risk analysis. Provides a foundation of basic theory and methodology as well as applied examples with techniques to analyzing large financial and econometric data. Hands-on experiments with R will be emphasized throughout the course. Offered by Systems Engr & Operations Rsch. Limited to two attempts. Equivalent to SYST 438.
Geophysical constraints on deep weathering and water storage potential in the Southern Sierra Critical Zone Observatory

The conversion of bedrock to regolith marks the inception of critical zone processes, but the factors that regulate it remain poorly understood. Although the thickness and degree of weathering of regolith are widely thought to be important regulators of the development of regolith and its water‐storage potential, the functional relationships between regolith properties and the processes that generate it remain poorly documented. This is due in part to the fact that regolith is difficult to characterize by direct observations over the broad scales needed for process‐based understanding of the critical zone. Here we use seismic refraction and resistivity imaging techniques to estimate variations in regolith thickness and porosity across a forested slope and swampy meadow in the Southern Sierra Critical Zone Observatory (SSCZO). Inferred seismic velocities and electrical resistivities image a weathering zone ranging in thickness from 10 to 35 m (average = 23 m) along one intensively studied transect. The inferred weathering zone consists of roughly equal thicknesses of saprolite (P‐velocity < 2 km s−1) and moderately weathered bedrock (P‐velocity = 2–4 km s−1). A minimum‐porosity model assuming dry pore space shows porosities as high as 50% near the surface, decreasing to near zero at the base of weathered rock. Physical properties of saprolite samples from hand augering and push cores are consistent with our rock physics model when variations in pore saturation are taken into account. Our results indicate that saprolite is a crucial reservoir of water, potentially storing an average of 3 m3 m−2 of water along a forested slope in the headwaters of the SSCZO. When coupled with published erosion rates from cosmogenic nuclides, our geophysical estimates of weathering zone thickness imply regolith residence times on the order of 105 years. Thus, soils at the surface today may integrate weathering over glacial–interglacial fluctuations in climate. Copyright © 2013 John Wiley & Sons, Ltd.
Bacterial Endophytic Communities in the Grapevine Depend on Pest Management

Microbial plant endophytes are receiving ever-increasing attention as a result of compelling evidence regarding functional interaction with the host plant. Microbial communities in plants were recently reported to be influenced by numerous environmental and anthropogenic factors, including soil and pest management. In this study we used automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and pyrosequencing of 16S rDNA to assess the effect of organic production and integrated pest management (IPM) on bacterial endophytic communities in two widespread grapevines cultivars (Merlot and Chardonnay). High levels of the dominant Ralstonia, Burkholderia and Pseudomonas genera were detected in all the samples We found differences in the composition of endophytic communities in grapevines cultivated using organic production and IPM. Operational taxonomic units (OTUs) assigned to the Mesorhizobium, Caulobacter and Staphylococcus genera were relatively more abundant in plants from organic vineyards, while Ralstonia, Burkholderia and Stenotrophomonas were more abundant in grapevines from IPM vineyards. Minor differences in bacterial endophytic communities were also found in the grapevines of the two cultivars.
Effects of Nonlinear Training with Resistance Exercise on Breast Cancer Survivor with Lymphedema and Hypothyroidism during Adjuvant Hormone Therapy: A Case Study

Exercise is considered capable of optimizing the immune system and minimizing the side effects of adjuvant and neoadjuvant therapies in cancer (BC) survivors. Despite these findings, the effects of nonlinear resistance training (NLRT) on breast cancer (BC) survivors with lymphedema have not yet been elucidated. Thus, the aim of this study was to evaluate the effects of 12 weeks of NLRT, three times a week, on lipid and hormonal profiles, body composition and anthropometric indices, muscle strength and endurance, aerobic performance, and blood pressure (BP) and mean arterial pressure (MAP) in a BC survivor with lymphedema and hypothyroidism under hormonotherapy. A 43 years old female, diagnosed with an invasive ductal and triple positive (PR+ and RE+) BC three years ago, lymphedema two years ago and hypothyroidism 9 years ago, under use of Tamoxifen (20 mg/day) for 3 years (hormonotherapy) and Euthyrox (25 mg/day) for 9 years, was assessed before and after each resistance training. There was improvement in lipid and hormonal profiles, anthropometric indices, upper and lower limb strength and endurance, and resting BP and MAP. Although there was no difference in physical fitness in a 6-minute walk test, the heart rate decreased during this test. The application of NLRT for 12 weeks was beneficial and safe in a BC survivor undergoing hormonotherapy.
Inferring Causalities in Landscape Genetics: An Extension of Wright’s Causal Modeling to Distance Matrices

Identifying landscape features that affect functional connectivity among populations is a major challenge in fundamental and applied sciences. Landscape genetics combines landscape and genetic data to address this issue, with the main objective of disentangling direct and indirect relationships among an intricate set of variables. Causal modeling has strong potential to address the complex nature of landscape genetic data sets. However, this statistical approach was not initially developed to address the pairwise distance matrices commonly used in landscape genetics. Here, we aimed to extend the applicability of two causal modeling methods—that is, maximum-likelihood path analysis and the directional separation test—by developing statistical approaches aimed at handling distance matrices and improving functional connectivity inference. Using simulations, we showed that these approaches greatly improved the robustness of the absolute (using a frequentist approach) and relative (using an information-theoretic approach) fits of the tested models. We used an empirical data set combining genetic information on a freshwater fish species (Gobio occitaniae) and detailed landscape descriptors to demonstrate the usefulness of causal modeling to identify functional connectivity in wild populations. Specifically, we demonstrated how direct and indirect relationships involving altitude, temperature, and oxygen concentration influenced within- and between-population genetic diversity of G. occitaniae.
Sensitive Leptospira DNA detection using tapered optical fiber sensor

This paper presents the development of tapered optical fiber sensor to detect a specific Leptospira bacteria DNA. The bacteria causes Leptospirosis, a deadly disease but with common early flu‐like symptoms. Optical single mode fiber (SMF) of 125 μm diameter is tapered to produce 12 μm waist diameter and 15 cm length. The novel DNA‐based optical fiber sensor is functionalized by incubating the tapered region with sodium hydroxide (NaOH), (3‐Aminopropyl) triethoxysilane and glutaraldehyde. Probe DNA is immobilized onto the tapered region and subsequently hybridized by its complementary DNA (cDNA). The transmission spectra of the DNA‐based optical fiber sensor are measured in the 1500 to 1600 nm wavelength range. It is discovered that the shift of the wavelength in the SMF sensor is linearly proportional with the increase in the cDNA concentrations from 0.1 to 1.0 nM. The sensitivity of the sensor toward DNA is measured to be 1.2862 nm/nM and able to detect as low as 0.1 fM. The sensor indicates high specificity when only minimal shift is detected for non‐cDNA testing. The developed sensor is able to distinguish between actual DNA of Leptospira serovars (Canicola and Copenhageni) against Clostridium difficile (control sample) at very low (femtomolar) target concentrations.
Determination of the starting dose in the first-in-human clinical trials with monoclonal antibodies: a systematic review of papers published between 1990 and 2013

A systematic review was performed to evaluate how the maximum recommended starting dose (MRSD) was determined in first-in-human (FIH) studies with monoclonal antibodies (mAbs). Factors associated with the choice of each MRSD determination method were also identified. PubMed was searched for FIH studies with mAbs published in English between January 1, 1990 and December 31, 2013, and the following information was extracted: MRSD determination method, publication year, therapeutic area, antibody type, safety factor, safety assessment results after the first dose, and number of dose escalation steps. Seventy-nine FIH studies with mAbs were identified, 49 of which clearly reported the MRSD determination method. The no observed adverse effects level (NOAEL)-based approach was the most frequently used method, whereas the model-based approach was the least commonly used method (34.7% vs 16.3%). The minimal anticipated biological effect level (MABEL)- or minimum effective dose (MED)-based approach was used more frequently in 2011–2013 than in 1990–2007 (31.6% vs 6.3%, P=0.036), reflecting a slow, but steady acceptance of the European Medicines Agency’s guidance on mitigating risks for FIH clinical trials (2007). The median safety factor was much lower for the MABEL- or MED-based approach than for the other MRSD determination methods (10 vs 32.2–53). The number of dose escalation steps was not significantly different among the different MRSD determination methods. The MABEL-based approach appears to be safer and as efficient as the other MRSD determination methods for achieving the objectives of FIH studies with mAbs faster.
Cost-effectiveness of pertuzumab combined with trastuzumab and docetaxel as a first-line treatment for HER-2 positive metastatic breast cancer

ABSTRACT Objective: To provide perspective for the National Health Insurance Bureau (NHIB), we determined the cost-effectiveness of pertuzumab combined with trastuzumab and docetaxel (TDP) versus trastuzumab and docetaxel (TD) as a first-line treatment for HER-2 positive metastatic breast cancer. Methods: We used a Markov model to simulate cost-effectiveness, disease progression, and survival, based on clinical data and transition probabilities extracted from the CLEOPATRA study. Direct medical costs were acquired from the NHIB claims database.The utilities in health state were based on a recent cost-effectiveness study on trastuzumab and pertuzumab. Outcomes included quality-adjusted life-years (QALYs), costs in New Taiwan dollars (NT$), and the incremental cost-effectiveness ratio (ICER). We performed one-way deterministic and probabilistic sensitivity analyses to assess the impact of specific parameters on the model. Results: Modeled median survival was 39.1 months for TD and 50.1 months for TDP. The ICER was NT$18,999,687 (US$593,741) per QALY gained. The sensitivity analyses indicated that TDP could be cost-effective under favorable assumptions; TDP had a 68% chance of being cost-effective, if TDP costs could be reduced with 10% in the stable disease state. Conclusion: Our model predicted that TDP would be cost-effective as a first-line treatment for HER-2 positive metastatic breast cancer, but only under favorable drug cost assumptions.
Association between obesity and asthma – epidemiology, pathophysiology and clinical profile

Abstract Obesity is a risk factor for asthma, and obese asthmatics have lower disease control and increased symptom severity. Several putative links have been proposed, including genetics, mechanical restriction of the chest and the intake of corticosteroids. The most consistent evidence, however, comes from studies of cytokines produced by the adipose tissue called adipokines. Adipokine imbalance is associated with both proinflammatory status and asthma. Although reverse causation has been proposed, it is now acknowledged that obesity precedes asthma symptoms. Nevertheless, prenatal origins of both conditions complicate the search for causality. There is a confirmed role of neuro-immune cross-talk mediating obesity-induced asthma, with leptin playing a key role in these processes. Obesity-induced asthma is now considered a distinct asthma phenotype. In fact, it is one of the most important determinants of asthma phenotypes. Two main subphenotypes have been distinguished. The first phenotype, which affects adult women, is characterised by later onset and is more likely to be non-atopic. The childhood obesity-induced asthma phenotype is characterised by primary and predominantly atopic asthma. In obesity-induced asthma, the immune responses are shifted towards T helper (Th) 1 polarisation rather than the typical atopic Th2 immunological profile. Moreover, obese asthmatics might respond differently to environmental triggers. The high cost of treatment of obesity-related asthma, and the burden it causes for the patients and their families call for urgent intervention. Phenotype-specific approaches seem to be crucial for the success of prevention and treatment.
Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. This method has been shown to perform well in analyses of simulated and empirical molecular sequence datasets where evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of datasets. Until now, however, RelTime has been used without a mathematical foundation. Here, we show that a relative rate framework (RRF) combined with the principle of minimum rate change among ancestral and descendant lineages forms the primary basis of RelTime divergence time estimation. Under this framework, we present analytical solutions for estimating relative lineage rates and divergence times. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. The mathematical foundation and computational efficiency makes RRF suitable not only for the analysis of molecular sequence datasets, but also analyzing phylogenies where branch lengths reflect evolutionary changes at levels other than nucleotide or protein sequence, such as external morphology or biochemical traits.
Computational Methods for High-Throughput Small RNA Analysis in Plants

Plants can show long-term effects of environmental stresses and in some cases a stress “memory” has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear if or how epigenetic mechanisms are involved. Here, we show that the composition of small regulatory RNAs in apomictic dandelion lineages reveals a footprint of drought stress and salicylic acid treatment experienced two generations ago. Overall proportions of 21 and 24 nt RNA pools were shifted due to grandparental treatments. While individual genes did not show strong up-or downregulation of associated sRNAs, the subset of genes that showed the strongest shifts in sRNA abundance was significantly enriched for several GO terms including stress-specific functions. This suggests that a stress-induced signal was transmitted across multiple unexposed generations leading to persistent changes in epigenetic gene regulation.
Research on stability and nonlinear vibration of shape memory alloy hybrid laminated composite panel under aerodynamic and thermal loads

The stability and nonlinear vibration of a NiTi shape memory alloy hybrid laminated composite panel under aerodynamic and thermal loads are investigated. The partial differential dynamic equations of the shape memory alloy hybrid laminated composite panel are derived based on the large deformation theory, the first-order piston theory of aerodynamic pressure and a simple constitutive model of shape memory alloy. Then, the general expressions of multimode discrete equations of the shape memory alloy hybrid laminated composite panel are obtained for the first time using Galerkin method. The stability of the shape memory alloy hybrid laminated composite panel is analyzed first based on the Routh–Hurwitz criteria, and the results show that the temperature and aerodynamic pressure parameter plane can be divided into a flat and stable region, a flutter region, and a buckling region, and the flat and stable region can be greatly enlarged as the shape memory alloy volume fraction increases. Meanwhile, numerical results of the dynamic equations show that the shape memory alloy hybrid laminated composite panel can produce various dynamic motions, and the bifurcation characteristics of the responses with temperature obtained by numerical method coincide well with the stability boundaries determined by analytical method.
Folic acid delays development of atherosclerosis in low‐density lipoprotein receptor‐deficient mice

Many studies support the cardioprotective effects of folic acid (FA). We aimed to evaluate the utility of FA supplementation in preventing the development of atherosclerotic in low‐density lipoprotein receptor‐deficient (LDLR−/−) mice and to elucidate the molecular processes underlying this effect. LDLR−/− mice were randomly distributed into four groups: control group, HF group, HF + FA group and the HF + RAPA group. vascular smooth muscle cells (VSMCs) were divided into the following four groups: control group, PDGF group, PDGF + FA group and PDGF + FA + RAPA group. Blood lipid levels, oxidative stress and inflammatory cytokines were measured. Atherosclerosis severity was evaluated with oil red O staining. Haematoxylin and eosin (H&E) staining was used to assess atherosclerosis progression. Immunohistochemical staining was performed with antismooth muscle α‐actin (α‐SMA) antibodies and anti‐osteopontin (OPN) antibodies that demonstrate VSMC dedifferentiation. The protein expression of α‐SMA, OPN and mechanistic target of rapamycin (mTOR)/p70S6K signalling was detected by Western blot analysis. FA and rapamycin reduced serum levels of total cholesterol, triacylglycerol, LDL, inhibiting oxidative stress and the inflammatory response. Oil red O and H&E staining demonstrated that FA and rapamycin inhibited atherosclerosis. FA and rapamycin treatment inhibited VSMC dedifferentiation in vitro and in vivo, and FA and rapamycin attenuated the mTOR/p70S6K signalling pathway. Our findings suggest that FA attenuates atherosclerosis development and inhibits VSMC dedifferentiation in high‐fat‐fed LDLR−/− mice by reduced lipid levels and inhibiting oxidative stress and the inflammatory response through mTOR/p70S6K signalling pathway.
The Role of the Wearable Cardioverter-Defibrillator In Contemporary Clinical Practice

The implantable cardioverter-defibrillator (ICD) has been shown to improve survival in patients at high risk for sudden cardiac arrest (SCA). However, there remain situations in which an ICD may be inappropriate: the high risk for SCA is temporary, there is need for interruption of implanted ICD therapy (e.g. for infection), there is temporary inability to implant an ICD, there is bridge period to heart transplant, or there is refusal of an indicated ICD. In these situations a wearable cardioverter-defibrillator (WCD) can be used to protect against SCA during the bridging period. We review the potential role of the WCD in clinical practice and summarize the published studies detailing the use of the WCD.