Miracle-dz/UniFAR-FTUs huggingface dataset:
On the problem of confounders in modeling gene expression

Motivation: Modeling of Transcription Factor (TF) binding from both ChIP‐seq and chromatin accessibility data has become prevalent in computational biology. Several models have been proposed to generate new hypotheses on transcriptional regulation. However, there is no distinct approach to derive TF binding scores from ChIP‐seq and open chromatin experiments. Here, we review biases of various scoring approaches and their effects on the interpretation and reliability of predictive gene expression models. Results: We generated predictive models for gene expression using ChIP‐seq and DNase1‐seq data from DEEP and ENCODE. Via randomization experiments, we identified confounders in TF gene scores derived from both ChIP‐seq and DNase1‐seq data. We reviewed correction approaches for both data types, which reduced the influence of identified confounders without harm to model performance. Also, our analyses highlighted further quality control measures, in addition to model performance, that may help to assure model reliability and to avoid misinterpretation in future studies. Availability and implementation: The software used in this study is available online at https://github.com/SchulzLab/TEPIC. Supplementary information: Supplementary data are available at Bioinformatics online.
Triamcinolone acetonide intralesional injection for the treatment of keloid scars: patient selection and perspectives

Keloids are pathological scars presenting as nodular lesions that extend beyond the area of injury. They do not spontaneously regress, often continuing to grow over time. The abnormal wound-healing process underlying keloid formation results from the lack of control mechanisms self-regulating cell proliferation and tissue repair. Keloids may lead to cosmetic disfigurement and functional impairment and affect the quality of life. Although several treatments were reported in the literature, no universally effective therapy was found to date. The most common approach is intralesional corticosteroid injection alone or in combination with other treatment modalities. Triamcinolone acetonide (TAC) is the most commonly used intralesional corticosteroid. The aim of this article was to review the use of TAC, alone or in combination, in the treatment of keloid scars. The response to corticosteroid injection alone is variable with 50–100% regression and a recurrence rate of 33% and 50% after 1 and 5 years, respectively. Compared to verapamil, TAC showed a faster and more effective response even though with a higher complication rate. TAC combined with verapamil was proved to be effective with statistically significant overall improvements of scars over time and long-term stable results. TAC and 5-fluorouracil (5-FU) intralesional injections were found to achieve comparable outcomes when administered alone, although 5-FU was more frequently associated with side effects. Conversely, the combination of 5-FU and TAC was more effective and showed fewer undesirable effects compared to TAC or 5-FU alone. Several kinds of laser treatments were reported to address keloids; however, laser therapy alone was burdened with a high recurrence rate. Better results were described by combining CO2, pulsed-dye or Nd: YAG lasers with TAC intralesional injections. Further options such as needle-less intraepidermal drug delivery are being explored, but more studies are needed to establish safety, feasibility and effectiveness of this approach.
A Standardized Approach to Cesarean Surgical Technique and Its Effect on Operative Time and Surgical Morbidity

Abstract Objective To evaluate the impact of a standardized surgical technique for primary cesarean deliveries (CDs) on operative time and surgical morbidity. Materials and Methods Two-year retrospective chart review of primary CD performed around the implementation of a standardized CD surgical technique. The primary outcome was total operative time (TOT). Secondary outcomes included incision-to-delivery time (ITDT), surgical site infection, blood loss, and maternal and fetal injuries. Results When comparing pre- versus postimplementation surgical times, there was no significant difference in TOT (76.5 vs. 75.9 minutes, respectively; p = 0.42) or ITDT (9.8 vs. 8.8 minutes, respectively; p = 0.06) when the entire cohort was analyzed. Subgroup analysis of CD performed early versus late in an academic year among the pre- and postimplementation groups showed no significant difference in TOT (79.3 early vs. 73.8 minutes late; p = 0.10) or ITDT (10.8 early vs. 8.8 minutes late; p = 0.06) within the preimplementation group. In the postimplementation group, however, there was significant decrease in TOT (80.5 early vs. 71.3 minutes late; p = 0.02) and ITDT (10.6 early vs. 6.8 minutes late; p < 0.01). Secondary outcomes were similar for both groups. Conclusion A standardized surgical technique combined with surgical experience can decrease TOT and ITDT in primary CD without increasing maternal morbidity.
Feature Clustering for Anomaly Detection Using Improved Fuzzy Membership Function

Earlier research focus towards anomaly detection has been towards using classifiers such as kNN, SVM and using existing distance measures to perform classification. Traditionally IDSs (Intrusion detection systems) have been developed by applying machine learning techniques and adopted single learning mechanism. This is later extended by developing Intrusion Detection Systems by adopting multiple learning mechanisms. Such systems have addressed better detection rates compared to single learning Intrusion Detection Systems. Dimensionality is one more serious concern which affects the performance of classification algorithms. Approaches such as "Feature selection" have been studied and adopted which selects a subset features from the feature set. However, the feature extraction approach for dimensionality reduction has proved to be better compared to feature selection and achieved better classification and detection rates. In this research, we address "Feature extraction" using "Evolutionary feature clustering" by proposing a "Novel fuzzy membership function" which addresses Dimensionality Reduction (DR). The idea is to transform the initial connection representation so that its equivalent representation has reduced noise affect and achieves better classification or detection rates. Experimental results on KDD datasets with 19 and 41 attributes, prove that the proposed approach has improved detection rates for R2L and U2R attack classes when compared to CANN, CLAPP, and SVM approaches. CANN approach recorded lower detection rates w.r. t U2R and R2L attacks. This failure is addressed in our earlier studies through proposing, CLAPP which proved comparatively better accuracy rates to CANN. The fuzzy membership function proposed in this paper, recorded better classification and detection rates in experiments conducted
Scalability Analysis of a LoRa Network Under Imperfect Orthogonality

Low-power wide-area network (LPWAN) technologies are gaining momentum for Internet-of-things applications since they promise wide coverage to a massive number of battery operated devices using grant-free medium access. LoRaWAN, with its physical (PHY) layer design and regulatory efforts, has emerged as the widely adopted LPWAN solution. By using chirp spread spectrum modulation with qausi-orthogonal spreading factors (SFs), LoRa PHY offers coverage to wide-area applications while supporting high-density of devices. However, thus far its scalability performance has been inadequately modeled and the effect of interference resulting from the imperfect orthogonality of the SFs has not been considered. In this paper, we present an analytical model of a single-cell LoRa system that accounts for the impact of interference among transmissions over the same SF (co-SF) as well as different SFs (inter-SF). By modeling the interference field as Poisson point process under duty cycled ALOHA, we derive the signal-to-interference ratio distributions for several interference conditions. Results show that, for a duty cycle as low as 0.33%, the network performance under co-SF interference alone is considerably optimistic as the inclusion of inter-SF interference unveils a further drop in the success probability and the coverage probability of approximately 10% and 15%, respectively, for 1500 devices in a LoRa channel. Finally, we illustrate how our analysis can characterize the critical device density with respect to cell size for a given reliability target.
The present and future use of functional near‐infrared spectroscopy (fNIRS) for cognitive neuroscience

The past few decades have seen a rapid increase in the use of functional near‐infrared spectroscopy (fNIRS) in cognitive neuroscience. This fast growth is due to the several advances that fNIRS offers over the other neuroimaging modalities such as functional magnetic resonance imaging and electroencephalography/magnetoencephalography. In particular, fNIRS is harmless, tolerant to bodily movements, and highly portable, being suitable for all possible participant populations, from newborns to the elderly and experimental settings, both inside and outside the laboratory. In this review we aim to provide a comprehensive and state‐of‐the‐art review of fNIRS basics, technical developments, and applications. In particular, we discuss some of the open challenges and the potential of fNIRS for cognitive neuroscience research, with a particular focus on neuroimaging in naturalistic environments and social cognitive neuroscience.
Genome-Wide Characterization of DNA Demethylase Genes and Their Association with Salt Response in Pyrus

DNA methylation plays important roles in genome protection and the regulation of gene expression and it is associated with plants’ responses to environments. DNA demethylases are very important proteins in DNA methylation regulation. In this study, we performed genome-wide and deep analysis of putative demethylases (DMEs) in pear. Seven DME genes were found in the pear genome and were defined as PbDME1–7 based on their domain organization. Results were supported by the gene structural characteristics and phylogenetic analysis. The gene structure of the DME genes were relatively complex and the DME7 proteins didn’t contain the Perm_CXXC domain. The DME genes experienced a whole genome duplication event (WGD) that occurred in the ancestor genome of pear and apple before their divergence based on the Ks values. Expression results showed that high salinity stress could influence the expression level of DMEs and salt-responsive genes in Pyrus betulaefolia. Furthermore, the methylation levels of salt-responsive genes changed under salt stress treatment. Results suggested important roles of PbDME genes in response to salt stress and are useful for better understanding the complex functions of this DME genes, which will facilitate epigenetic studies in pear trees salt tolerance.
Acute hemodynamic effects of methylxanthine therapy in preterm neonates: Effect of variations in subgroups.

BACKGROUND Methylxanthines have cardiac stimulant effects. The current study aimed to compare acute hemodynamic changes between caffeine and aminophylline in ≤34 weeks' preterm neonates. METHODS The study was performed using information on echocardiography measurements from preterm neonates recruited for apnea of prematurity (75 of 240) and preventing extubation failure (113 of 156) studies. The neonates were randomized either to the caffeine or aminophylline groups. Neonates with no maintenance followed by loading doses with both the methylxanthines (caffeine and aminophylline) and incomplete echocardiography examination were excluded. RESULTS Cardiac parameters were found to be similar between groups. The heart rate was higher among the aminophylline-treated neonates (p < 0.001) than among the caffeine-treated ones. End-systolic volume was higher among both caffeine- (p < 0.001) and aminophylline-treated neonates (p = 0.001) when compared with pretreatment values. End-diastolic volume was statistically higher in both groups' neonates (p = 0.01). The odds of increase in cardiac output was higher; however, increase in ejection fraction was less in caffeine-treated small-for-gestation-age neonates. CONCLUSION Caffeine has similar effects on cardiac parameters as aminophylline; however, caffeine-treated small-for-gestation stratification gave rise to significant cardiac variations.
Ecotoxicology and Environmental Safety

An increasing input rate of rare earth elements in the environment is expected because of the intense extraction of such elements form their ores to face human technological needs. In this study Lemna minor L. plants were grown under laboratory conditions and treated with increasing concentrations of cerium (Ce) ions to investigate the e ﬀ ects on plant growth and antioxidant systems. The growth increased in plants treated with lower Ce concentrations and reduced in plants treated with higher concentrations, compared to control plants. In plants treated with higher Ce concentrations lower levels of chlorophyll and carotenoid and the appearance of chlorotic symptoms were also detected. Increased levels of hydrogen peroxide, antioxidant metabolites and antioxidant activity con ﬁ rmed that higher Ce concentrations are toxic to L. minor . Ce concentration in plant tissues was also determined and detectable levels were found only in plants grown on Ce-supplemented media. The use of duckweed plants as a tool for biomonitoring of Ce in freshwater is discussed.
JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell lung cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Interestingly, although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed. In addition, a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and independent manner.
An Optimized Robot-Based Technique for Cochlear Implantation to Reduce Array Insertion Trauma

Objective To compare the intracochlear trauma induced by optimized robot-based and manual techniques with a straight electrode array prototype inserted at different lengths. Study Design Experimental study. Setting Robot-based otologic surgery laboratory. Subjects and Methods A prototype array was inserted at different insertion lengths (21 and 25 mm) in 20 temporal bones. The manual insertion was performed with a microforceps. The optimized approach consisted of an optimal axis insertion provided by a robot-based arm controlled by a tracking system, with a constant speed of insertion (0.25 mm/s) achieved by a motorized insertion tool. The electrode position was determined at the level of each electrode by stereomicroscopic cochlea section analysis. Results A higher number of electrodes correctly located in the scala tympani was associated with the optimized approach (P = .03, 2-way analysis of variance). Regardless of the insertion technique used, the array inserted at 25 mm allowed complete insertion of the active stimulating portion of the array in all cases. Insertion depth was greater when the array was inserted to 25 mm versus 21 mm (P < .001, 2-way analysis of variance). The optimized insertion was associated with less trauma than that from manual insertion regardless the length of the inserted array (P = .04, 2-way analysis of variance). Conclusion Compared with a manual insertion, intracochlear trauma could be reduced with array insertion performed on an optimal axis by using motorized insertion and by applying a constant insertion speed.
Lossy Hyperspectral Image Compression Based on Intraband Prediction and Inter-band Fractal

Fractal encoding promising proficiency in area of picture compressing but not used at compression of hyperspectral images. The paper presents a novel and applicable copy hyperspectral image lossy compressing founded in intra-prediction fractals bandwidth and hybrid between bands. The hyper spectral color picture is divided to different groups of bandings (GOB). So, the intraband estimate is used the first banding to each one GOB, overworking the spatial relation, as the form encrypting between banding through a resident exploration procedure is used to other bands at apiece (GOB), maximizing resident likeness among two together banding. The fractals constraints is contracted with coded Exponential-Golomb coding entropies. So, progress the decrypted value, the forecast mistake and the remaining fractal transform, quantize and encoded into entropy. Experimental compression results show that our scheme can achieve a actual high peak signal-to-noise ratio (PSNR) at low-slung bit degree and achieve a medium PSNR increase taking into account the overall bit complexity encoding rates compared to other lossless compression methods. Furthermore, the classification of the accuracy of our reconstructed image is 99.75%, which is better than the original uncompressed image.
ZFYVE26/SPASTIZIN and SPG11/SPATACSIN mutations in hereditary spastic paraplegia types AR-SPG15 and AR-SPG11 have different effects on autophagy and endocytosis

ABSTRACT ZFYVE26/Spastizin and SPG11/Spatacsin encode 2 large proteins that are mutated in hereditary autosomal-recessive spastic paraplegia/paraparesis (HSP) type 15 (AR-SPG15) and type 11 (AR-SPG11), respectively. We previously have reported that AR-SPG15-related ZFYVE26 mutations lead to autophagy defects with accumulation of immature autophagosomes. ZFYVE26 and SPG11 were found to be part of a complex including the AP5 (adaptor related protein complex 5) and to have a critical role in autophagic lysosomal reformation with identification of autophagic and lysosomal defects in cells with both AR-SPG15- and AR-SPG11-related mutations. In spite of these similarities between the 2 proteins, here we report that ZFYVE26 and SPG11 are differently involved in autophagy and endocytosis. We found that both ZFYVE26 and SPG11 interact with RAB5A and RAB11, 2 proteins regulating endosome trafficking and maturation, but only ZFYVE26 mutations affected RAB protein interactions and activation. ZFYVE26 mutations lead to defects in the fusion between autophagosomes and endosomes, while SPG11 mutations do not affect this step and lead to a milder autophagy defect. We thus demonstrate that ZFYVE26 and SPG11 affect the same cellular physiological processes, albeit at different levels: both proteins have a role in autophagic lysosome reformation, but only ZFYVE26 acts at the intersection between endocytosis and autophagy, thus representing a key player in these 2 processes. Indeed expression of the constitutively active form of RAB5A in cells with AR-SPG15-related mutations partially rescues the autophagy defect. Finally the model we propose demonstrates that autophagy and the endolysosomal pathway are central processes in the pathogenesis of these complicated forms of hereditary spastic paraparesis. Abbreviations: ALR, autophagic lysosome reformation; AP5, adaptor related protein complex 5; AR, autosomal-recessive; HSP, hereditary spastic paraplegia/paraparesis; ATG14, autophagy related 14; BafA, bafilomycin A1; BECN1, beclin 1; EBSS, Earle balanced salt solution; EEA1, early endosome antigen 1; EGF, epidermal growth factor; EGFR, epidermal growth factor receptor; GDP, guanosine diphosphate; GFP, green fluorescent protein; GTP, guanosine triphosphate; HSP, hereditary spastic paraplegias; LBPA, lysobisphosphatidic acid; MAP1LC3B/LC3B, microtubule associated protein 1 light chain 3 beta; MVBs, multivesicular bodies; PIK3C3, phosphatidylinositol 3-kinase, catalytic subunit type 3; PIK3R4, phosphoinositide-3-kinase regulatory subunit 4; PtdIns3P, phosphatidylinositol-3-phosphate; RFP, red fluorescent protein; RUBCN, RUN and cysteine rich domain containing beclin 1 interacting protein; shRNA, short hairpin RNA; SQSTM1/p62, sequestosome 1; TCC: thin corpus callosum; TF, transferrin; UVRAG, UV radiation resistance associated.
Socio-demographic determinants of obesity indexes in Iran: findings from a nationwide STEPS survey

Background: Overweight and obesity are considered as non-communicable diseases (NCDs) risk factors with increasing prevalence worldwide. This nationwide study aimed to determine the socio-demographic determinants of obesity indexes in Iran. Methods: This cross-sectional study was conducted based on data from the sixth round of nationwide Stepwise approach to surveillance (STEPS) survey in the 31 provinces of Iran in 2011. A total of 9878 people aged ≥20 years were selected using a multi-stage cluster sampling method. Data were collected through three steps questionnaire including ecological, physical and biochemical measurements. We assessed body mass index (BMI), waist circumference(WC) and waist-hip ratio (WHR) as the main indicators of obesity. Results: In this study, the weighted prevalence of overweight and obesity were 34.5% (95% CI:33.6, 35.5) and 21.5% (95% CI: 20.7, 22.3), respectively. The mean ± standard deviation (SD)of BMI among men and women were 25.4±4.4 and 26.9±5.2 kg/m2 respectively. Older age,living alone, having lower education level, being housewife or retired were associated with overweight and obesity (P<0.05). Urbanization was positively associated with BMI and WC.Being obese or overweight was associated with having a history of type 2 diabetes mellitus (T2DM), hypertension (HTN) and cardiovascular diseases (CVDs). Conclusion: The prevalence of overweight in this study was less than global rate while it was vice versa for obesity prevalence. Some socio-demographic characteristics were identified as determinants of obesity which should be considered for planning preventive and control action plans.
Touch with foreign hands: the effect of virtual hand appearance on visual-haptic integration

Hand tracking and haptics are gaining more importance as key technologies of virtual reality (VR) systems. For designing such systems, it is fundamental to understand how the appearance of the virtual hands influences user experience and how the human brain integrates vision and haptics. However, it is currently unknown whether multi-sensory integration of visual and haptic feedback can be influenced by the appearance of virtual hands in VR. We performed a user study in VR to gain insight into the effect of hand appearance on how the brain combines visual and haptic signals using a cue-conflict paradigm. In this paper, we show that the detection of surface irregularities (bumps and holes) sensed by eyes and hands is affected by the rendering of avatar hands. However, sensitivity changes do not correlate with the degree of perceived limb ownership. Qualitative feedback provides insights into potentially distracting cues in visual-haptic integration.