Miracle-dz/UniFAR-FTUs huggingface dataset:
Maternal Residential Proximity to Hazardous Waste Sites and Risk for Selected Congenital Malformations

Using data from two population‐based case‐control studies, we investigated whether maternal residential proximity to hazardous waste sites increased the risk for neural tube defects, conotruncal heart defects, and oral cleft defects in California. We obtained a residential history by interview for mothers of 507 neural tube defect cases (82.7% of eligible) and their 517 controls (84.6%); and 201 heart cases (84.4%), 439 cleft cases (82.2%), and their 455 controls (72.1%). We identified the locations of 764 inactive hazardous waste sites and systematically collected information on site‐related contamination for the subset of 105 National Priority List sites. After controlling for several potential confounders, we found little or no increased risk for maternal residence in a census tract containing a site [odds ratio (OR) = 0.9, 95% confidence interval (CI) = 0.7–1.3 for neural tube defects; OR = 1.3, 95% CI = 0.8–2.1 for heart cases; OR = 1.2, 95% CI = 0.8–1.8 for clefts], but elevated risks for neural tube defects (OR = 2.1, 95% CI = 0.6–7.6) and heart defects (OR = 4.2, 95% CI = 0.7–26.5) for maternal residence within 1/4 mile of a National Priority List site. Furthermore, we observed elevated ORs (≥2.0) for neural tube defects and heart defects in association with maternal residence within 1 mile of National Priority List sites containing selected chemical contaminants. Among controls, only 0.6% and 4.4% lived within 1/4 mile and 1 mile of a National Priority List site, respectively, resulting in imprecision in risk estimation.
Bayesian Experimental Design of Magnetic Resonance Imaging Sequences

We show how improved sequences for magnetic resonance imaging can be found through optimization of Bayesian design scores. Combining approximate Bayesian inference and natural image statistics with high-performance numerical computation, we propose the first Bayesian experimental design framework for this problem of high relevance to clinical and brain research. Our solution requires large-scale approximate inference for dense, non-Gaussian models. We propose a novel scalable variational inference algorithm, and show how powerful methods of numerical mathematics can be modified to compute primitives in our framework. Our approach is evaluated on raw data from a 3T MR scanner.
Disruption of Telomere–Telomere Interactions Associated with DNA Damage in Human Spermatozoa

Telomeres play a fundamental role in the organization of the sperm nucleus resulting in the looped chromosome configuration and non-random positioning of chromosomes. Telomeres localize in the nuclear periphery and interact dynamically by forming dimers and tetramers. The purpose of this study was to evaluate the relationship of telomere interactions to DNA damage, a factor known to adversely influence male fertility. Telomeres were localized by fluorescence in situ hybridization (FISH) using human chromosome pan-telomeric probe in ten samples with low and ten samples with high sperm DNA damage. The samples with a low DNA fragmentation index (DFI) had a mean number of telomere signals of 21.7±1.9 compared to a mean of 26.5±3.4 signals in the samples with a high DFI (p<.005). The percentage of cells with a typical telomere distribution of ≤23 telomere-telomere dimers was observed in 70.8%±15.6 samples with a low DFI compared to 44.2%±22.4 in samples with a high DFI (p<.05). These results suggest that sperm DNA damage is associated with disruption of the normal telomere–telomere interactions leading to possible loss of the looped chromosome configuration. Improperly packed and organized sperm chromatin might have a high probability of disrupting the extremely structured sequence of sperm chromosome deposition, activation, and processing by the oocyte at the time of fertilization. These results might provide additional information on the nature of sperm DNA damage and the role of such damage on fertilization and development of the zygote.
Components of Care Vary in Importance for Overall Patient-Reported Experience by Type of Hospitalization

Background:Patients are hospitalized for disparate conditions and procedures. Patient experiences with care may depend on hospitalization type (HT). Objectives:Determine whether the contributions of patient experience composite measures to overall hospital ratings on the Hospital Consumer Assessment of Healthcare Providers and Systems Survey vary by HT. Research Design:In cross-sectional observational data, we defined 24 HTs using major diagnostic category and service line (medical, surgical, or obstetrical). To assess the importance of each composite for each HT, we calculated the simultaneous partial correlations of 7 composite scores with an overall hospital rating, controlling for patient demographics. Subjects:Nineteen thousand seven hundred twenty English- or Spanish-speaking adults with nonpsychiatric primary diagnoses discharged home 12/02-1/03 after an overnight inpatient stay in any of 132 general acute care hospitals in 3 states. Measures:Patient-reported doctor communication, nurse communication, staff responsiveness, physical environment, new medicines explained, pain control, and postdischarge information; overall 0 to 10 rating of care. Results:Nurse communication was most important overall, with a 0.34 average partial correlation (range: 0.17-0.49; P < 0.05 and among the 3 most important composites for all HTs). Discharge information was least important (0.05 average partial correlation; P < 0.05 for 10 of 24 HTs). Interactions demonstrated significant (P < 0.05) variation in partial correlations by HT for 5 of 7 composites (all but responsiveness and environment), with nurse communication, doctor communication, and pain control showing the most variation (F > 2, P < 0.05). Conclusions:The importance of patient experience dimensions differs substantially and varies by HT. Quality improvement efforts should target those aspects of patient experience that matter most for each HT.
Label-free Quantitative Proteomics Reveals Differentially Regulated Proteins Influencing Urolithiasis

Urinary proteins have been implicated as inhibitors of kidney stone formation (urolithiasis). As a proximal fluid, prefiltered by the kidneys, urine is an attractive biofluid for proteomic analysis in urologic conditions. However, it is necessary to correct for variations in urinary concentration. In our study, individual urine samples were normalized for this variation by using a total protein to creatinine ratio. Pooled urine samples were compared in two independent experiments. Differences between the urinary proteome of stone formers and nonstone-forming controls were characterized and quantified using label-free nano-ultraperformance liquid chromatography high/low collision energy switching analysis. There were 1063 proteins identified, of which 367 were unique to the stone former groups, 408 proteins were unique to the control pools, and 288 proteins were identified for comparative quantification. Proteins found to be unique in stone-formers were involved in carbohydrate metabolism pathways and associated with disease states. Thirty-four proteins demonstrated a consistent >twofold change between stone formers and controls. For ceruloplasmin, one of the proteins was shown to be more than twofold up-regulated in the stone-former pools, this observation was validated in individuals by enzyme-linked immunosorbent assay. Moreover, in vitro crystallization assays demonstrated ceruloplasmin had a dose-dependent increase on calcium oxalate crystal formation. Taken together, these results may suggest a functional role for ceruloplasmin in urolithiasis.
Resveratrol Prevents Estrogen-DNA Adduct Formation and Neoplastic Transformation in MCF-10F Cells

Abstract Exposure to estrogens is a risk factor for breast cancer. Specific estrogen metabolites may initiate breast cancer and other cancers. Genotoxicity may be caused by cytochrome P450 (CYP)–mediated oxidation of catechol estrogens to quinones that react with DNA to form depurinating estrogen-DNA adducts. CYP1B1 favors quinone formation by catalyzing estrogen 4-hydroxylation, whereas NAD(P)H quinone oxidoreductase 1 (NQO1) catalyzes the protective reduction of quinones to catechols. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) induces CYP1B1 expression through the aryl hydrocarbon receptor (AhR). Resveratrol has anticancer effects in diverse in vitro and in vivo systems and is an AhR antagonist that decreases CYP expression but induces NQO1 expression. The chemopreventive effect of resveratrol on breast cancer initiation was investigated in MCF-10F cells. Its effects on estrogen metabolism and formation of estrogen-DNA adducts were analyzed in culture medium by high-performance liquid chromatography, whereas its effects on CYP1B1 and NQO1 were determined by immunoblotting and immunostaining. The antitransformation effects of resveratrol were also examined. TCDD induced expression of CYP1B1 and its redistribution in the nucleus and cytoplasm. Concomitant treatment with resveratrol dose-dependently suppressed TCDD-induced expression of CYP1B1, mainly in the cytoplasm. Resveratrol dose- and time-dependently induced expression of NQO1. NQO1 is mainly in the perinuclear membrane of control cells, but resveratrol induced NQO1 and its intracellular redistribution, which involves nuclear translocation of nuclear factor erythroid 2–related factor 2. Resveratrol decreased estrogen metabolism and blocked formation of DNA adducts in cells treated with TCDD and/or estradiol. Resveratrol also suppressed TCDD and/or estradiol-induced cell transformation. Thus, resveratrol can prevent breast cancer initiation by blocking multiple sites in the estrogen genotoxicity pathway.
Exploring Relationships between Canopy Architecture, Light Distribution, and Photosynthesis in Contrasting Rice Genotypes Using 3D Canopy Reconstruction

The arrangement of leaf material is critical in determining the light environment, and subsequently the photosynthetic productivity of complex crop canopies. However, links between specific canopy architectural traits and photosynthetic productivity across a wide genetic background are poorly understood for field grown crops. The architecture of five genetically diverse rice varieties—four parental founders of a multi-parent advanced generation intercross (MAGIC) population plus a high yielding Philippine variety (IR64)—was captured at two different growth stages using a method for digital plant reconstruction based on stereocameras. Ray tracing was employed to explore the effects of canopy architecture on the resulting light environment in high-resolution, whilst gas exchange measurements were combined with an empirical model of photosynthesis to calculate an estimated carbon gain and total light interception. To further test the impact of different dynamic light patterns on photosynthetic properties, an empirical model of photosynthetic acclimation was employed to predict the optimal light-saturated photosynthesis rate (Pmax) throughout canopy depth, hypothesizing that light is the sole determinant of productivity in these conditions. First, we show that a plant type with steeper leaf angles allows more efficient penetration of light into lower canopy layers and this, in turn, leads to a greater photosynthetic potential. Second the predicted optimal Pmax responds in a manner that is consistent with fractional interception and leaf area index across this germplasm. However, measured Pmax, especially in lower layers, was consistently higher than the optimal Pmax indicating factors other than light determine photosynthesis profiles. Lastly, varieties with more upright architecture exhibit higher maximum quantum yield of photosynthesis indicating a canopy-level impact on photosynthetic efficiency.
Coping styles in families with haemophilia

This study explored the similarities and differences in the coping styles used by parents and children in families where there is a chronic illness, specifically the blood disorder haemophilia. The coping methods employed by each family member were determined by asking all subjects to complete a coping measure in relation to a problem they were currently experiencing. The two coping measures employed were The revised ways of coping checklist (Vitaliano et al., 1985) for the parents and the Kidcope (Spirito et al., 1988) for the children. Findings suggest that: most adults and children use all of the coping styles at least some of the time; there are no group gender differences in the coping styles used by parents; mothers and fathers in parental couples tend to use similar coping styles; children with and without a chronic illness show some differences in their coping styles, although there are also many similarities irrespective of illness status; there are important differences in the coping styles used by parents and children.
Blocking TGF-β Signaling Pathway Preserves Mitochondrial Proteostasis and Reduces Early Activation of PDGFRβ+ Pericytes in Aristolochic Acid Induced Acute Kidney Injury in Wistar Male Rats

Background The platelet-derived growth factor receptor β (PDGFRβ)+ perivascular cell activation becomes increasingly recognized as a main source of scar-associated kidney myofibroblasts and recently emerged as a new cellular therapeutic target. Aims In this regard, we first confirmed the presence of PDGFRβ+ perivascular cells in a human case of end-stage aristolochic acid nephropathy (AAN) and thereafter we focused on the early fibrosis events of transforming growth factor β (TGFβ) inhibition in a rat model of AAN. Materials and Methods Neutralizing anti-TGFβ antibody (1D11) and its control isotype (13C4) were administered (5 mg/kg, i.p.) at Days -1, 0, 2 and 4; AA (15 mg/kg, sc) was injected daily. Results At Day 5, 1D11 significantly suppressed p-Smad2/3 signaling pathway improving renal function impairment, reduced the score of acute tubular necrosis, peritubular capillaritis, interstitial inflammation and neoangiogenesis. 1D11 markedly decreased interstitial edema, disruption of tubular basement membrane loss of brush border, cytoplasmic edema and organelle ultrastructure alterations (mitochondrial disruption and endoplasmic reticulum edema) in proximal tubular epithelial cells. Moreover, 1D11 significantly inhibited p-PERK activation and attenuated dysregulation of unfolded protein response (UPR) pathways, endoplasmic reticulum and mitochondrial proteostasis in vivo and in vitro. Conclusions The early inhibition of p-Smad2/3 signaling pathway improved acute renal function impairment, partially prevented epithelial-endothelial axis activation by maintaining PTEC proteostasis and reduced early PDGFRβ+ pericytes-derived myofibroblasts accumulation.
Toward a programmable software-defined IoT architecture for sensor service provision on demand

In the age of Internet of Things (IoT), sensors form a foundational component of IoT services, yet they are rigid with little capability for programmable configuration or reusability as they are application-specific, manufacturer-specific. Emerging IoT applications often deploy a vast number of sensors which may serve multiple applications. Programmability is thus essential but not found in legacy or current generation sensors. It is challenging to effectively utilize heterogeneity of resources to handle a large number of application demands. Software Defined Networking (SDN) and Network Function Virtualization (NFV) have proved effective paradigms for provisioning services on-demand and managing network functions and their life cycles. This paper proposes a software defined IoT architecture that captures the spirit of SDN and NFV where a software-defined Internet of Things (SD-IoT) controller can provide services as requested by an application and also manage heterogeneous physical sensors through their virtual representation called software-defined virtual sensor (SD-VSensor) autonomously. In particular, the paper presents the design of a streamline SD-IoT controller, a lightweight and reconfigurable SD-VSensor, and the communication protocol (S-MANAGE) between them. The proposed architecture enables heterogeneous application-specific WSN systems to be recognized and effectively utilized by diverse IoT applications under the orchestration of the SD-IoT controller. Moreover, heterogeneity of sensor nodes or IoT devices can be programmed to achieve sensor services on demand. The preliminary implementation results demonstrate the feasibility and efficiency of the proposed architecture.
Design and Evaluation of a Flexible-Bandwidth OFDM-Based Intra-Data Center Interconnect

Data center networks are facing growing challenges to deliver higher bandwidth efficiency, lower latency, better flexibility, and lower cost. Various optical interconnect schemes have been proposed to take advantage of the high bandwidth capacity and low power consumption offered by optical switching. However, these schemes cannot offer flexible bandwidth sharing due to the large granularity in optical circuit switching, and they require costly optical components. In this paper, we introduce a novel data center network architecture based on cyclic arrayed waveguide grating device and multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing technology with parallel signal detection (PSD). This architecture offers flexible bandwidth resource sharing at fine granularity. Other features include high-speed switching, low and uniform latency, and the ability to change the data rates dynamically. By eliminating costly optical components and keeping the core optical router passive and static, the power consumption, hardware cost, and operation cost are reduced. The fine granularity bandwidth sharing and MIMO switching through PSD are verified experimentally. We also propose and evaluate efficient subcarrier allocation schemes to achieve high bandwidth utilization. Finally, we present the implementation of an efficient scheduler for the bandwidth allocation of the proposed scheme.
Family Background Variables as Instruments for Education in Income Regressions: A Bayesian Analysis

Abstract The validity of family background variables instrumenting education in income regressions has been much criticized. In this paper, we use data from the 2004 German Socio-Economic Panel and Bayesian analysis to analyze to what degree violations of the strict validity assumption affect the estimation results. We show that, in case of moderate direct effects of the instrument on the dependent variable, the results do not deviate much from the benchmark case of no such effect (perfect validity of the instrument's exclusion restriction). In many cases, the size of the bias is smaller than the width of the 95% posterior interval for the effect of education on income. Thus, a violation of the strict validity assumption does not necessarily lead to results which are strongly different from those of the strict validity case. This finding provides confidence in the use of family background variables as instruments in income regressions.
Simiduia agarivorans gen. nov., sp. nov., a marine, agarolytic bacterium isolated from shallow coastal water from Keelung, Taiwan.

A Gram-negative, heterotrophic, agarolytic, marine bacterium, designated strain SA1T, was isolated from a seawater sample collected in the shallow coastal region of Keelung, Taiwan. Cells were straight to slightly curved rods. Nearly all of the cells were non-motile and non-flagellated during the exponential phase of growth in broth cultures; a few cells (<1 %) were motile and were considered to have monotrichous flagella. The isolate required NaCl for growth and grew optimally at 30-35 degrees C and 2-3 % (w/v) NaCl. It grew aerobically and was incapable of anaerobic growth by fermentation of glucose or other carbohydrates. However, anaerobic growth could be achieved by reduction of nitrate to nitrite. Polar lipids comprised phosphatidylethanolamine (71.8 %), diphosphatidylglycerol (12.7 %), phosphatidylglycerol (12.2 %) and phosphatidylserine (3.3 %). Isoprenoid quinones consisted of Q-10 (87.5 %), MK-9 (6.6 %) and MK-7 (5.9 %). Major cellular fatty acids were C16 : 1 omega 7c and/or iso-C15 : 0 2-OH (28.6 %), C17 : 1 omega 8c (22.8 %), C16 : 0 (14.5 %), C18 : 1 omega 7c (11.0 %) and C17 : 0 (6.4 %). The DNA G+C content was 55.6 mol%. Phylogeny based on 16S rRNA gene sequence analysis showed that strain SA1T formed a distinct lineage within the class Gammaproteobacteria. Strain SA1T was related most closely to Teredinibacter turnerae, Cellvibrio spp. , Saccharophagus degradans, Pseudomonas spp. and Microbulbifer spp. , strains of these species sharing <93 % 16S rRNA gene sequence similarity with strain SA1T. The phylogenetic data and those from physiological, morphological and chemotaxonomic characterizations indicated that strain SA1T represents a novel species and genus, for which the name Simiduia agarivorans gen. nov., sp. nov. is proposed. The type strain is SA1T (=BCRC 17597T=JCM 13881T).
Metabolic syndrome in young women with the polycystic ovary syndrome: revisiting the threshold for an abnormally decreased high‐density lipoprotein cholesterol serum level

Please cite this paper as: Dewailly D, Contestin M, Gallo C, Catteau‐Jonard S. Metabolic syndrome in young women with the polycystic ovary syndrome: revisiting the threshold for an abnormally decreased high‐density lipoprotein cholesterol serum level. BJOG 2010;117:175–180.
The identification of phosducin as a novel candidate gene for hypertension and its role in sympathetic activation

Purpose of reviewThe primary objective of this review is to familiarize readers with the recent identification of phosducin (Pdc) as a novel candidate gene for stress-induced hypertension using comparative genetics and the elucidation of its role in sympathetic activation. Recent findingsPhosducin was previously identified as a G-protein regulator expressed in the retina and pineal gland. Knowledge of its physiological role as a G-protein regulator was limited. A recent study by Beetz et al. based on comparative genetics of mice and humans establishes Pdc as a novel candidate gene for stress-induced hypertension. This study further delineates the role of phosducin as a regulator of sympathetic activity in postsynaptic ganglia and highlights the importance of sympathetic function in blood pressure regulation. In addition, it demonstrates the utility of the complementary approaches of population-based association testing and animal model genetics in the discovery of genes for complex phenotypes. SummaryThe identification of Pdc as a gene for stress-induced hypertension offers new insights into the relationship between sympathetic nervous system activation, blood pressure regulation and genetic factors. It has implications for both the treatment of hypertension and kidney disease and may represent a new target for novel therapeutics.
Key sharing scheme based on one weighted threshold secret sharing

Secret sharing scheme is a cryptographic technology that safely manages password keys by dividing them into segments. Existing (k, n) threshold secret sharing scheme has a problem of allowing recovery of original secret information by collecting k or more random segments among divided secret information segments. To resolve such problem, this paper proposes a one weighted threshold secret sharing scheme. That is, by granting weighted value on a secret segment, original secret information cannot be recovered by collecting k or more segments, as long as the segment applied with weighted value is not included in the collection.