Miracle-dz/UniFAR-FTUs huggingface dataset:
Characteristics of Severe Retinopathy of Prematurity in Infants with Birth Weight above 1500 Grams at a Referral Center in Turkey

Purpose To demonstrate the clinical characteristics and treatment outcomes of severe retinopathy of prematurity (ROP) in preterm infants with birth weight (BW) above 1500 g in Turkey. Methods A retrospective review of 5920 ROP records was performed in Zeynep Kamil Maternity and Children’s Diseases Training and Research Hospital. The records were obtained from ROP treatment center of the same institute between 2011 and 2016. The data comprised the demographic and clinical characteristics including, gestational age, BW, systemic risk factors, zone and stage of ROP, ROP type, treatment modality, treatment outcomes and inborn/outborn status of the babies. Results A total of 36 infants (71 eyes) with severe ROP and BW> 1500 g were retrieved. There were 30 infants (83.3%) with type 1 ROP and 6 infants (16.7%) with aggressive posterior ROP (APROP). 3 infants (8.3%) were born at our hospital whereas 33 (91.7%) were referred from outer private neonatal intensive care unit (NICU) centers. Zone I APROP was detected during the initial screening. 21 infants (58.3%) underwent laser treatment while 15 (41.7%) received intravitreal bevacizumab (IVB) injections. No unfavorable structural outcome was observed following either treatment modality. Conclusion Severe ROP may occur in heavier preterm infants. Laser treatment and IVB injections were useful in selected cases. Presence of APROP at first examination suggests an earlier screening in heavier babies. Standardization of private NICU centers as well as establishing a national ROP protocol is necessary in Turkey.
Low-δ18O Rhyolites from Yellowstone: Magmatic Evolution Based on Analyses of Zircons and Individual Phenocrysts

The Yellowstone Plateau volcanic field is one of the largest centers exchange time to form zoned zircons is between a few hundred and a few thousand years, which reflects the residence time of lowO of rhyolitic magmatism on Earth. Major caldera-forming eruptions are followed by unusual lowO rhyolites. New oxygen isotope, magmas after formation and before eruption. petrologic and geochemical data from rhyolites belonging to the 2·0 my eruptive history of Yellowstone are presented, with emphasis on the genesis of lowO magmas erupted after the Huckleberry Ridge Tuff (2·0 Ma, 2500 km) and Lava Creek Tuff (0·6 Ma,
A Query Based Approach for Mining Evolving Graphs

An evolving graph is a graph that can change over time. Such graphs can be applied in modelling a wide range of real-world phenomena, like computer networks, social networks and protein interaction networks. This paper addresses the novel problem of querying evolving graphs using spatio-temporal patterns. In particular, we focus on answering selection queries, which can discover evolving subgraphs that satisfy both a temporal and a spatial predicate. We investigate the efficient implementation of such queries and experimentally evaluate our techniques using real-world evolving graph datasets --- Internet connectivity logs and the Enron email corpus. We show that is possible to use queries to discover meaningful events hidden in this data and demonstrate that our implementation is scalable for very large evolving graphs.
Direct Comparison between Critical Cooling Rate and Some Quantitative Parameters for Evaluation of Glass-Forming Ability in Pd-Cu-Ni-P Alloys

The quantitative parameters such as supercooled liquid region or several reduced glass transition temperatures were applied for evaluating the glass-forming ability of Pd-based metallic glasses. A distinct proportional tendency was recognized between measured critical cooling rates and reduced glass transition temperature by liquidus temperature rather than eutectic temperature. Significance and physical meanings of the quantitative parameters for evaluating of glass-forming ability were also discussed. Furthermore, a new concept of a modified reduced glass transition temperature was proposed to evaluate the glass-forming ability. The modified reduced glass transition temperature as a function of critical cooling rate was found to exhibit a much clear linearity.
Note Intensity Estimation of Piano Recordings by Score-Informed NMF

While dynamics is an important characteristic in music performance, it has been rarely researched in automatic music transcription. We propose a method to estimate individual note intensities from a piano recording given pre-aligned score data of the recording. To this end, we use non-negative matrix factorization in a score-informed framework, where the basis vectors and weights are constrained to estimate harmonic note spectra and corresponding intensities, respectively. We examine various choices in the learning process including the use of synthesized note scale for initialization, type of spectrum, and temporal constraint. We evaluate our method using Saarland Music Data (SMD) and estimate note intensities in MIDI velocity. The results show that the proposed method makes an improvement compared to previous work.
The contribution of phosphate–phosphate repulsions to the free energy of DNA bending

DNA bending is important for the packaging of genetic material, regulation of gene expression and interaction of nucleic acids with proteins. Consequently, it is of considerable interest to quantify the energetic factors that must be overcome to induce bending of DNA, such as base stacking and phosphate–phosphate repulsions. In the present work, the electrostatic contribution of phosphate–phosphate repulsions to the free energy of bending DNA is examined for 71 bp linear and bent-form model structures. The bent DNA model was based on the crystallographic structure of a full turn of DNA in a nucleosome core particle. A Green's function approach based on a linear-scaling smooth conductor-like screening model was applied to ascertain the contribution of individual phosphate–phosphate repulsions and overall electrostatic stabilization in aqueous solution. The effect of charge neutralization by site-bound ions was considered using Monte Carlo simulation to characterize the distribution of ion occupations and contribution of phosphate repulsions to the free energy of bending as a function of counterion load. The calculations predict that the phosphate–phosphate repulsions account for ∼30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle.
Plasma klotho and mortality risk in older community-dwelling adults.

BACKGROUND The aging-suppressor gene klotho encodes a single-pass transmembrane protein that in mice is known to extend life span when overexpressed and resemble accelerated aging when expression is disrupted. It is not known whether there is a relationship between plasma levels of secreted klotho protein and longevity in humans. METHODS We measured plasma klotho in 804 adults, greater than or equal to 65 years, in the InCHIANTI study, a longitudinal population-based study of aging in Tuscany, Italy. RESULTS During 6 years of follow-up, 194 (24.1%) of the participants died. In a multivariate Cox proportional hazards model, adjusting for age, sex, education, body mass index, physical activity, total cholesterol, high-density lipoprotein cholesterol, cognition, 25-hydroxyvitamin D, parathyroid hormone, serum calcium, mean arterial pressure, and chronic diseases, participants in the lowest tertile of plasma klotho (<575 pg/mL) had an increased risk of death compared with participants in the highest tertile of plasma klotho (>763 pg/mL; hazards ratio 1.78, 95% confidence interval 1.20-2.63). CONCLUSIONS In older community-dwelling adults, plasma klotho is an independent predictor of all-cause mortality. Further studies are needed to elucidate the potential biological mechanisms by which circulating klotho could affect longevity in humans.
Health and Quality of Life Outcomes Physical activity as a mediator of the impact of chronic conditions on quality of life in older adults

Background: Chronic conditions could negatively affect the quality of life of older adults. This may be partially due to a relative lack of physical activity. We examined whether physical activity mediates the relationship between different chronic conditions and several health outcomes that are important to the quality of life of older adults. Methods: The data were taken from the Canadian Community Health Survey (cycle 1.1), a cross-section survey completed in 2001. Only respondents who were 65 years or older were included in our study ( N = 22,432). The Health Utilities Index Mark 3 (HUI3) was used to measure overall quality of life, and to measure selected health outcomes (dexterity, mobility, pain, cognition, and emotional wellbeing) that are considered to be of importance to the quality of life of older adults. Leisure-time physical activity was assessed by determining weekly energy expenditure (Kcal per week) based on the metabolic equivalents of self-reported leisure activities. Linear and logistic regression models were used to determine the mediating effect of leisure-time physical activity while controlling for demographic variables (age and sex), substance use (tobacco use and alcohol consumption), and obesity. Results: Having a chronic condition was associated with a relative decrease in health utility scores and a relative increase in mobility limitations, dexterity problems, pain, emotional problems (i.e., decreased happiness), and cognitive limitations. These negative consequences could be partially attributed to a relative lack of physical activity in older adults with a chronic condition (14% mediation for the HUI3 score). The corresponding degree of mediation was 18% for mobility limitations, 5% for pain, and 13% for emotional wellbeing (statistically significant mediation was not observed for the other health attributes). These values varied with respect to the different chronic conditions examined in our study. Conclusion: Older adults with chronic conditions are less likely to engage in leisure-time physical activities of at least 1,000 Kcal per week, and this association partially accounts for some negative consequences of chronic conditions, including mobility limitations, pain, and emotional problems. These findings provide support for health promotion programs that facilitate or encourage increased leisure-time physical activity in older people with chronic conditions.
Electrochemical sensing of glucose using polyaniline nanofiber dendrites‐amperometric and impedimetric analysis

A novel electrochemical synthesis of polyaniline (PANI) nanofiber dendrites on platinum electrodes using p-toluenesulfonic acid for sensing of glucose is reported. The characterization of PANI is carried out using scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, and ultraviolet (UV)–visible spectral studies. The electrochemical behavior of the PANI-coated electrode is investigated with the help of cyclic voltammetry, chronoamperometry, and impedance spectroscopy, regarding its efficacy as a glucose sensor. The amperometric analysis shows a very low detection limit of ∼100 nM with the linear regime spanning 50 µM–12 mM, while the response time is <5 s. The Michaelis–Menten constant is estimated as 1.24 × 10−2 M indicating the high activity of the glucose oxidase enzyme. The equivalent circuit fitting of the Nyquist and Bode' plots is carried out to estimate the system parameters. The reliability of the PANI coated electrodes is demonstrated by procuring the authentic samples from the hospitals. The stability and reproducibility of the sensor is also analyzed. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Effects of Dietary Phosphate on Adynamic Bone Disease in Rats with Chronic Kidney Disease – Role of Sclerostin?

High phosphate intake is known to aggravate renal osteodystrophy along various pathogenetic pathways. Recent studies have raised the possibility that dysregulation of the osteocyte Wnt/β-catenin signaling pathway is also involved in chronic kidney disease (CKD)-related bone disease. We investigated the role of dietary phosphate and its possible interaction with this pathway in an experimental model of adynamic bone disease (ABD) in association with CKD and hypoparathyroidism. Partial nephrectomy (Nx) and total parathyroidectomy (PTx) were performed in male Wistar rats. Control rats with normal kidney and parathyroid function underwent sham operations. Rats were divided into three groups and underwent pair-feeding for 8 weeks with diets containing either 0.6% or 1.2% phosphate: sham 0.6%, Nx+PTx 0.6%, and Nx+PTx 1.2%. In the two Nx+PTx groups, serum creatinine increased and blood ionized calcium decreased compared with sham control group. They also presented hyperphosphatemia and reduced serum parathyroid hormone (PTH) and fibroblast growth factor 23 (FGF23) levels. Fractional urinary excretion of phosphate increased in Nx+PTx 1.2% rats despite lower PTH and FGF23 levels than in sham group. These biochemical changes were accompanied by a decrease in bone formation rates. The Nx+PTx 1.2% group had lower bone volume (BV/TV), higher osteoblast and osteocyte apoptosis, and higher SOST and Dickkopf-1 gene expression than the Nx+PTx 0.6% group. Nx+PTx 0.6% rat had very low serum sclerostin levels, and Nx+PTx 1.2% had intermediate sclerostin levels compared with sham group. Finally, there was a negative correlation between BV/TV and serum sclerostin. These results suggest that high dietary phosphate intake decreases bone volume in an experimental model of CKD-ABD, possibly via changes in SOST expression through a PTH-independent mechanism. These findings could have relevance for the clinical setting of CKD-ABD in patients who low turnover bone disease might be attenuated by optimal control of phosphate intake and/or absorption.
The structure and property of the electrospinning silk fibroin/gelatin blend nanofibers

Abstract Nanofibers could provide benefits due to high surface area for biomaterial scaffolds. In order to improve both silk fibroin and gelatin performance for potential biomedical applications, in this article the electrospinning of silk fibroin (SF)/gelatin (GT) blends with different composition ratio and concentration was performed with formic acid as a spinning solvent. The nanofibers morphologies and diameters were observed by Scanning electron microscopy (SEM). Blending with GT could improve the viscosity and spinnability of spinning solution. As-spun SF/GT blend nanofibers were more homogeneous and non-beaded than pure SF nanofibers. The diameter decreased with higher voltage at same electric field intensity. On increasing the concentrations of spinning solution, the pore diameter of nanofibers decreased, and the porosity increased. In addition, FTIR and DTA analyses showed SF/GT nanofibers had more β-sheets than pure SF nanofibers, which may be caused by an intermolecular interaction between SF and GT. Blending with GT also led to substantial enhancement in mechanical properties of SF nanofibers.
Cellular Adhesion Promotes Prostate Cancer Cells Escape from Dormancy

Dissemination of prostate cancer (PCa) cells to the bone marrow is an early event in the disease process. In some patients, disseminated tumor cells (DTC) proliferate to form active metastases after a prolonged period of undetectable disease known as tumor dormancy. Identifying mechanisms of PCa dormancy and reactivation remain a challenge partly due to the lack of in vitro models. Here, we characterized in vitro PCa dormancy-reactivation by inducing cells from three patient-derived xenograft (PDX) lines to proliferate through tumor cell contact with each other and with bone marrow stroma. Proliferating PCa cells demonstrated tumor cell-cell contact and integrin clustering by immunofluorescence. Global gene expression analyses on proliferating cells cultured on bone marrow stroma revealed a downregulation of TGFB2 in all of the three proliferating PCa PDX lines when compared to their non-proliferating counterparts. Furthermore, constitutive activation of myosin light chain kinase (MLCK), a downstream effector of integrin-beta1 and TGF-beta2, in non-proliferating cells promoted cell proliferation. This cell proliferation was associated with an upregulation of CDK6 and a downregulation of E2F4. Taken together, our data provide the first clinically relevant in vitro model to support cellular adhesion and downregulation of TGFB2 as a potential mechanism by which PCa cells may escape from dormancy. Targeting the TGF-beta2-associated mechanism could provide novel opportunities to prevent lethal PCa metastasis.
Evaluation of survival and success rates of dental implants placed at the time of or after alveolar ridge augmentation with an autogenous mandibular bone graft and titanium mesh: a 3- to 8-year retrospective study.

PURPOSE The purpose of this retrospective longitudinal study was to evaluate the survival and success rates of 56 implants consecutively placed in alveolar ridges following a one- or two-stage augmentative procedure, using autogenous bone and titanium micromeshes. MATERIALS AND METHODS This study included 24 consecutive patients treated with 27 micromeshes and mandibular particulated bone. In 13 patients, 20 implants were placed at the time of the reconstructive procedure. In the remaining 11 patients, 36 implants were positioned in a second surgery 8 to 9 months after grafting. Follow-up data (implant survival, success rate, marginal bone resorption) were collected after 3 to 8 years of prosthetic loading. RESULTS Four of the 27 micromeshes (complication rate, 14.8%) were exposed prematurely and were removed before the intended time. The mean vertical bone augmentation obtained was 5.4 +/- 1.81 mm for implants placed in simultaneous procedures and 4.5 +/- 1.16 mm in delayed procedures. None of the 56 implants was lost during the observation period (cumulative implant survival rate, 100%). Radiographic analysis showed stable marginal bone levels, with a mean bone resorption of 1.58 +/- 0.48 mm after 3 to 8 years. Only two implants demonstrated increased bone loss (3.12 and 3.37 mm) over the follow-up period, whereas the remaining 54 implants were considered clinically successful, resulting in a cumulative success rate of 96.4%. CONCLUSIONS This study revealed that implant placement in augmented ridges using micromeshes and autogenous bone provided satisfactory long-term survival and success rates, with minimal bone resorption.
of the Annual Meeting of the Cognitive Science Society Title Visual Context Effects on Thematic Role Assignment in Children versus Adults : Evidence from Eye Tracking in German Permalink

Prior research has shown that adults can make rapid use of visual context information (e.g., visual referential contrast and depicted agent-action-patient events) for syntactic structuring and disambiguation. By contrast, little is known about how visual context influences children’s language comprehension, and some results even suggest children cannot use visual referential context for syntactic structuring (e.g., Trueswell et al., 1999). We examined whether children (unlike adults) also struggle to use other kinds of information in visual context (e.g., depicted events) for real-time language comprehension. In two eye-tracking studies we directly compared real-time effects of depicted events on children’s (Exp1) vs. adults’ (Exp2) processing of spoken German subject-verb-object (SVO) and object-verb-subject (OVS) sentences. Both of these word orders are grammatical, but OVS is a non-canonical structure. Five-year olds are at chance in understanding even unambiguous OVS sentences in the absence of visual context (Dittmar et al., 2008). If children can use depicted events rapidly for syntactic structuring, we should find similar visual context effects for them as have been reported for adults (Knoeferle et al., 2005), and similar gaze pattern as for the adults in the present studies. Gaze pattern in the present studies suggested that events depicting who-does-what-to-whom incrementally influenced both adults’ and 5-year-olds’ visual attention and thematic role assignment. Depicted-event information helped children to get rid of their initial preference for the preferred SVO structure when interpreting OVS sentences. However, visual context effects were subtly delayed in children (vs. adults), and varied as a function of their accuracy and cognitive capacity.
Tubulin Post-Translational Modifications and Microtubule Dynamics

Microtubules are hollow tube-like polymeric structures composed of α,β-tubulin heterodimers. They play an important role in numerous cellular processes, including intracellular transport, cell motility and segregation of the chromosomes during cell division. Moreover, microtubule doublets or triplets form a scaffold of a cilium, centriole and basal body, respectively. To perform such diverse functions microtubules have to differ in their properties. Post-translational modifications are one of the factors that affect the properties of the tubulin polymer. Here we focus on the direct and indirect effects of post-translational modifications of tubulin on microtubule dynamics.
Structured Denoising Autoencoder for Fault Detection and Analysis

This paper proposes a new fault detection and analysis approach which can leverage incomplete prior information. Conventional data-driven approaches suer from the problem of overtting and result in high rates of false positives, and model-driven approaches suer from a lack of specic information about complex systems. We overcome these problems by modifying the denoising autoencoder (DA), a data-driven method, to form a new approach, called the structured denoising autoencoder (StrDA), which can utilize incomplete prior information. The StrDA does not require specic information and can perform well without overtting. In particular, an empirical analysis with synthetic data revealed that the StrDA performs better than the DA even when there is partially incorrect or abstract information. An evaluation using real data from moving cars also showed that the StrDA with incomplete knowledge outperformed conventional methods. Surprisingly, the StrDA results were better even though the parameters of the conventional methods were tuned using faulty data, which are normally unknown. In addition, the StrDA fault analysis was able to extract the true causes of the faulty data; the other methods were unable to do this. Thus, only our proposed method can explain why the faults occurred.