Miracle-dz/UniFAR-FTUs huggingface dataset:
Variations of hepcidin and iron‐status parameters during the menstrual cycle in healthy women

Hepcidin is the central regulator of systemic iron metabolism (Ganz, 2013). In clinical practice, measurements of serum hepcidin (SH) could help to determine the cause of anaemia, iron deficiency and iron overload, to predict iron absorption from food, to optimize the treatment of haemochromatosis and to manage erythropoietin therapy. Interpretation of SH measurement in practice will be dependent on understanding physiological variations of this hormone. Previous studies have suggested that SH varied according to a diurnal cycle (Ganz et al, 2008) and was modified by meals (Schaap et al, 2013). Gender should also be taken into account, as women tend to have lower hepcidin values than men. Moreover, in women, age should be also considered, because values of hepcidin are higher in postthan in pre-menopausal women. Nevertheless, iron status is the main determinant of SH concentration (Galesloot et al, 2011). Blood loss during menses, the main cause of iron deficiency in young women, varies between 20 and 80 ml during a period, representing a loss of 10–40 mg of iron in women with regular menstrual cycles (MC) (Higham et al, 1990). This is significant compared to the unregulated 1 mg eliminated daily through skin, intestinal and urinary cell desquamation, the only other physiological way to eliminate iron. To date, no study has examined whether menses induce significant variations in SH values. The present study (Clinical Trial.gov NCT01764412) was conducted in four French hospitals. Ninety healthy women, aged 18-45 years, with normal iron parameters, regular cycles and normal duration of menses (4 1 days) were included. Fifty-four used oral contraception. Transferrin saturation (TS), serum ferritin (SF), haemoglobin (Hb), serum iron (SI) and SH were measured at six visits distributed throughout the MC. All visits were planned on fasting subjects, between 8am and 9am. Day 0 was defined as the day after menses began. The following 3 visits were scheduled during menses and the following days. The last two visits took place respectively at the middle and at the end of the cycle. Serum hepcidin-25 was quantified using a CE-marked Enzyme Immunoassay (Bachem Inc., Torrance, CA, USA).
Automated Protein Subfamily Identification and Classification

Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in function prediction but has been difficult to automate for high-throughput application. To address this limitation, we present a computationally efficient pipeline for phylogenomic classification of proteins. This pipeline uses the SCI-PHY (Subfamily Classification in Phylogenomics) algorithm for automatic subfamily identification, followed by subfamily hidden Markov model (HMM) construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs enables classification of novel sequences to protein families and subfamilies. Sequences representing entirely novel subfamilies are differentiated from those that can be classified to subfamilies in the input training set using logistic regression. Subfamily HMM parameters are estimated using an information-sharing protocol, enabling subfamilies containing even a single sequence to benefit from conservation patterns defining the family as a whole or in related subfamilies. SCI-PHY subfamilies correspond closely to functional subtypes defined by experts and to conserved clades found by phylogenetic analysis. Extensive comparisons of subfamily and family HMM performances show that subfamily HMMs dramatically improve the separation between homologous and non-homologous proteins in sequence database searches. Subfamily HMMs also provide extremely high specificity of classification and can be used to predict entirely novel subtypes. The SCI-PHY Web server at http://phylogenomics.berkeley. edu/SCI-PHY/ allows users to upload a multiple sequence alignment for subfamily identification and subfamily HMM construction. Biologists wishing to provide their own subfamily definitions can do so. Source code is available on the Web page. The Berkeley Phylogenomics Group PhyloFacts resource contains pre-calculated subfamily predictions and subfamily HMMs for more than 40,000 protein families and domains at http://phylogenomics.berkeley. edu/phylofacts/.
Robustness of Rotation-Equivariant Networks to Adversarial Perturbations

Deep neural networks have been shown to be vulnerable to adversarial examples: very small perturbations of the input having a dramatic impact on the predictions. A wealth of adversarial attacks and distance metrics to quantify the similarity between natural and adversarial images have been proposed, recently enlarging the scope of adversarial examples with geometric transformations beyond pixel-wise attacks. In this context, we investigate the robustness to adversarial attacks of new Convolutional Neural Network architectures providing equivariance to rotations. We found that rotation-equivariant networks are significantly less vulnerable to geometric-based attacks than regular networks on the MNIST, CIFAR-10, and ImageNet datasets.
Advances and challenges: dendritic cell vaccination strategies for glioblastoma

ABSTRACT Introduction: Glioblastoma is the most common primary brain tumor in adults and prognosis remains poor with a median survival of approximately 15–17 months. This review provides an overview of recent advances in the field of glioblastoma immunotherapy. Areas covered: Recent advances in dendritic cell vaccination immunotherapy are showing encouraging results in clinical trials and promise to extend patient survival. In this report we discuss current scientific knowledge regarding dendritic cell (DC) vaccines, including approaches to differentiating, priming, and injecting dendritic cells to achieve maximal anti-tumor efficacy in glioblastoma. These findings are compared to recently completed and currently ongoing glioblastoma clinical trials. Novel methods such as ‘fastDCs’ and vaccines targeting DCs in-vivo may offer more effective treatment when compared to traditional DC vaccines and have already entered the clinic. Expert commentary: Finally, we discuss the challenges of T-cell dysfunctions caused by glioblastoma immunosuppression and how they affect dendritic cell vaccinations approaches.
Disordered high-frequency oscillation in face processing in schizophrenia patients

Abstract Schizophrenia is a complex disorder characterized by marked social dysfunctions, but the neural mechanism underlying this deficit is unknown. To investigate whether face-specific perceptual processes are influenced in schizophrenia patients, both face detection and configural analysis were assessed in normal individuals and schizophrenia patients by recording electroencephalogram (EEG) data. Here, a face processing model was built based on the frequency oscillations, and the evoked power (theta, alpha, and beta bands) and the induced power (gamma bands) were recorded while the subjects passively viewed face and nonface images presented in upright and inverted orientations. The healthy adults showed a significant face-specific effect in the alpha, beta, and gamma bands, and an inversion effect was observed in the gamma band in the occipital lobe and right temporal lobe. Importantly, the schizophrenia patients showed face-specific deficits in the low-frequency beta and gamma bands, and the face inversion effect in the gamma band was absent from the occipital lobe. All these results revealed face-specific processing in patients due to the disorder of high-frequency EEG, providing additional evidence to enrich future studies investigating neural mechanisms and serving as a marked diagnostic basis.
Usability inspection methods after 15 years of research and practice

Usability inspection methods, such as heuristic evaluation, the cognitive walkthrough, formal usability inspections, and the pluralistic usability walkthrough, were introduced fifteen years ago. Since then, these methods, analyses of their comparative effectiveness, and their use have evolved in different ways. In this paper, we track the fortunes of the methods and analyses, looking at which led to use and to further research, and which led to relative methodological dead ends. Heuristic evaluation and the cognitive walkthrough appear to be the most actively used and researched techniques. The pluralistic walkthrough remains a recognized technique, although not the subject of significant further study. Formal usability inspections appear to have been incorporated into other techniques or largely abandoned in practice. We conclude with lessons for practitioners and suggestions for future research.
The Root Aqueous Extract of Entada africana Guill. et Perr. (Mimosaceae) Inhibits Implant Growth, Alleviates Dysmenorrhea, and Restores Ovarian Dynamic in a Rat Model of Endometriosis

Entada africana (Mimosaceae) was reported to have analgesic and antioxidant properties. The present study is aimed at investigating the effects of the root aqueous extract of Entada africana (EA) on an experimental model of endometriosis. The study was performed in rats orally treated with EA at doses of 127.5, 255, and 510 mg/kg. Microgynon® 30 served as the reference substance. Estradiol valerate and oxytocin were used to induce dysmenorrhea. Endometrial implant levels of catalase and malondialdehyde (MDA) allowed estimating tissue oxidative status. Ovarian dynamic and rat sexual behavior were assessed through histological analysis of ovaries, uterus, and vagina. EA decreased dysmenorrhea at tested doses following a 7-day treatment (p < 0.001). Endometrial implant volume decreased following the three treatment periods (p < 0.05). Catalase activity (p < 0.001) and MDA level (p < 0.01) increased only following a 3-day treatment. EA also increased antral follicles, reduced luteinized unruptured follicle number (p < 0.001), and induced animals to be in the estrus phase. In conclusion, EA prevented the progress of endometriosis, reduced dysmenorrhea, promoted ovarian follicle growth, prevented anovulation, and stimulated the special period of rat sexual desire. These results suggest that Entada africana could be a promising alternative option for the treatment of endometriosis.
Eye gaze perception in bipolar disorder: Self‐referential bias but intact perceptual sensitivity

Deficits in social cognition predict poor functional outcome in severe mental illnesses such as schizophrenia and autism. However, research findings on social cognition in bipolar disorder (BD) are sparse and inconsistent. This study aimed to characterize a critical social cognitive process—eye gaze perception—and examine its functional correlates in BD to inform psychopathological mechanisms.
Integrated biocircuits: engineering functional multicellular circuits and devices

Objective. Implantable neurotechnologies have revolutionized neuromodulatory medicine for treating the dysfunction of diseased neural circuitry. However, challenges with biocompatibility and lack of full control over neural network communication and function limits the potential to create more stable and robust neuromodulation devices. Thus, we propose a platform technology of implantable and programmable cellular systems, namely Integrated Biocircuits, which use only cells as the functional components of the device. Approach. We envision the foundational principles for this concept begins with novel in vitro platforms used for the study and reconstruction of cellular circuitry. Additionally, recent advancements in organoid and 3D culture systems account for microenvironment factors of cytoarchitecture to construct multicellular circuits as they are normally formed in the brain. We explore the current state of the art of these platforms to provide knowledge of their advancements in circuit fabrication and identify the current biological principles that could be applied in designing integrated biocircuit devices. Main results. We have highlighted the exemplary methodologies and techniques of in vitro circuit fabrication and propose the integration of selected controllable parameters, which would be required in creating suitable biodevices. Significance. We provide our perspective and propose new insights into the future of neuromodulaion devices within the scope of living cellular systems that can be applied in designing more reliable and biocompatible stimulation-based neuroprosthetics.
Shikonin inhibits myeloid differentiation protein 2 to prevent LPS‐induced acute lung injury

Acute lung injury (ALI) is a challenging clinical syndrome, which manifests as an acute inflammatory response. Myeloid differentiation protein 2 (MD2) has an important role in mediating LPS‐induced inflammation. Currently, there are no effective molecular‐based therapies for ALI or viable biomarkers for predicting the severity of disease. Recent preclinical studies have shown that shikonin, a natural naphthoquinone, prevents LPS‐induced inflammation. However, little is known about the underlying mechanisms.
NT-proBNP has a high negative predictive value to rule-out short-term cardiovascular events in patients with diabetes mellitus.

AIMS This study evaluated the predictive value of NT-proBNP for patients with diabetes mellitus and compared the prognostic aptitude of this neurohumoral marker to traditional markers of cardiovascular events. METHODS AND RESULTS A prospective observational study was conducted in 631 diabetic patients. The composite endpoint consisted of unplanned hospitalization for cardiovascular events or death within the observation period of 12 months. Of all variables analysed (age, gender, history of hypertension, ischaemic heart disease/any cardiac disease, smoking, duration of diabetes, body mass index, blood pressure, New York Heart Association-class, Dyspnoea score, Minnesota Living with Heart Failure Questionnaire, LDL-cholesterol, HbA(1c), creatinine, glomerular filtration rate), the logarithm of NT-proBNP gave the most potent information in a stepwise Cox regression analysis (P < 0.0001). Bootstrapping with 500 samples supports this result in 95% samples. The negative predictive value of a normal value (<125 pg/mL) of NT-proBNP for short-term cardiovascular events in diabetic patients is 98%. CONCLUSION We have demonstrated a strong and independent correlation between NT-proBNP and short-term prognosis of cardiovascular events for patients with diabetes mellitus. With a high negative predictive value it can identify individuals who are not at intermediate risk for cardiovascular events. NT-proBNP proved to be of higher predictive value than traditional cardiovascular markers, in this unselected cohort.
The Budgeted Maximum Coverage Problem in Partially Deployed Software Defined Networks

Due to the large installed base of distributed legacy networks, software defined networking (SDN) nodes may be required to coexist with legacy nodes to form hybrid networks. It has been shown that such a hybrid network has better performance than a pure legacy network due to smarter transmission scheduling. Despite such advantages, limited budgets continue to hinder the rapid adaptation of SDNs. Only a part of the network can be upgraded at a time especially for large-scale networks. In this paper, we define the minimum percentage of SDN nodes in a path, and paths with at least one SDN node, as the hop coverage and path coverage, respectively. We intend to evaluate the relationship between cost and coverage in the partially deployed SDNs. We formulate SDN node selection as four optimization problems with hop/path coverage and cost as objectives and constraints, respectively, and vice-versa. We propose two heuristic solutions: 1) maximum number of uncovered path first (MUcPF) and 2) maximum number of minimum hop covered path first (MMHcPF), to these NP-hard problems. Through a MATLAB experiment, we show that MUcPF is significantly better in terms of economy and efficiency to establish a hybrid path between every pair of hosts in the network. In particular, it required 5%-15% less investment to achieve 100% path coverage compared to other algorithms. The results show the coverage consistency of MMHcPF on each individual path along with gains in terms of cost and efficiency. It takes 5%-20% less investment to achieve certain hop coverage target compared to other existing algorithms.
A product oriented approach to quantify usability attributes and the interactive quality of user interfaces.

Four different measures based on a product oriented view of user interfaces are introduced. Different types of user interfaces can be described and differentiated by the powerful concept of "interaction points". Regarding to the interactive semantic of "interaction points" (FIPs), 4 different types of FIPs must be discriminated. Based on the concept of interaction points, the dimensions "feedback", "interactive directness" and "flexibility" can be quantified. The results of a theoretical and an empirical validation of 4 quantitative measures are presented and discussed.
The neurobiology of emotion regulation in posttraumatic stress disorder: Amygdala downregulation via real‐time fMRI neurofeedback

Amygdala dysregulation has been shown to be central to the pathophysiology of posttraumatic stress disorder (PTSD) representing a critical treatment target. Here, amygdala downregulation was targeted using real‐time fMRI neurofeedback (rt‐fMRI‐nf) in patients with PTSD, allowing us to examine further the regulation of emotional states during symptom provocation. Patients (n = 10) completed three sessions of rt‐fMRI‐nf with the instruction to downregulate activation in the amygdala, while viewing personalized trauma words. Amygdala downregulation was assessed by contrasting (a) regulate trials, with (b) viewing trauma words and not attempting to regulate. Training was followed by one transfer run not involving neurofeedback. Generalized psychophysiological interaction (gPPI) and dynamic causal modeling (DCM) analyses were also computed to explore task‐based functional connectivity and causal structure, respectively. It was found that PTSD patients were able to successfully downregulate both right and left amygdala activation, showing sustained effects within the transfer run. Increased activation in the dorsolateral and ventrolateral prefrontal cortex (PFC), regions related to emotion regulation, was observed during regulate as compared with view conditions. Importantly, activation in the PFC, rostral anterior cingulate cortex, and the insula, were negatively correlated to PTSD dissociative symptoms in the transfer run. Increased functional connectivity between the amygdala‐ and both the dorsolateral and dorsomedial PFC was found during regulate, as compared with view conditions during neurofeedback training. Finally, our DCM analysis exploring directional structure suggested that amygdala downregulation involves both top‐down and bottom‐up information flow with regard to observed PFC‐amygdala connectivity. This is the first demonstration of successful downregulation of the amygdala using rt‐fMRI‐nf in PTSD, which was critically sustained in a subsequent transfer run without neurofeedback, and corresponded to increased connectivity with prefrontal regions involved in emotion regulation during the intervention. Hum Brain Mapp 38:541–560, 2017. © 2016 Wiley Periodicals, Inc.
Girdin protein: A potential metastasis predictor associated with prognosis in lung cancer

The present study explored the relationship between Girdin protein expression and the survival rate of patients with lung carcinoma. A total of 334 lung cancer specimens, 20 benign lung disease tissue sections and 24 fresh tissues from patients with lung carcinoma were analyzed by immunohistochemistry and western blotting. Girdin protein was expressed in 130/334 (38.93%) of the cases examined. Girdin protein expression was correlated with tumor/node/metastasis stage (P<0.001), lymph node metastasis (P=0.001), distant metastasis (P<0.001) and specimen sites (P=0.034). Girdin expression was also correlated with signal transducer and activator of transcription 3 (STAT3) expression (P<0.001). Patients with high Girdin and STAT3 expression had a significantly poorer prognosis compared with those with low/high, high/low or low/low expression (P<0.001). In summary, Girdin may be a prognostic marker of lung cancer and serve as a biomarker for metastasis.
Performance Investigation of an Exhaust Thermoelectric Generator for Military SUV Application

To analyze the thermoelectric power generation for sports utility vehicle (SUV) application, a novel thermoelectric generator (TEG) based on low-temperature Bi2Te3 thermoelectric modules (TEMs) and a chaos-shaped brass heat exchanger is constructed. The temperature distribution of the TEG is analyzed based on an experimental setup, and the temperature uniformity optimization method is performed by chipping peak off and filling valley is taken to validate the improved output power. An automobile exhaust thermoelectric generator (AETEG) using four TEGs connected thermally in parallel and electrically in series is assembled into a prototype military SUV, its temperature distribution, output voltage, output power, system efficiency, inner resistance, and backpressure is analyzed, and several important influencing factors such as vehicle speed, clamping pressure, engine coolant flow rate, and ambient temperature on its output performance are tested. Experimental results demonstrate that higher vehicle speed, larger clamping pressure, faster engine coolant flow rate and lower ambient temperature can enhance the overall output performance, but the ambient temperature and coolant flow rate are less significant. The maximum output power of AETEG is 646.26 W, the corresponding conversion efficiency is 1.03%, and the increased backpressure changes from 1681 Pa to 1807 Pa when the highest vehicle speed is 125 km/h.
High sensitive method for optical birefringence measurement

A sensitive method for optical birefringence measurement is presented. To optimize the signal over the noise ratio, the polarization of the laser beam is modulated exceptionally with a high frequency electro-optical modulator. The specially developed optical apparatus exhibits high sensitivity and accuracy, which were checked by measuring the Cotton-Mouton effect in nitrogen as a function of the pressure. It is able to measure the retardance down to 2x10-4 rad. This apparatus will be used with the locked optical cavity. The optical cavity will serve as an optical path multiplier for increasing the sensitivity. This proposed set-up will be able to measure the Cotton-Mouton effect in helium, where the birefringence effect is Δn ≈ 2.4x10-16.
Improved GQ-CNN: Deep Learning Model for Planning Robust Grasps

Recent developments in the field of robot grasping have shown great improvements in the grasp success rates when dealing with unknown objects. In this work we improve on one of the most promising approaches, the Grasp Quality Convolutional Neural Network (GQ-CNN) trained on the DexNet 2.0 dataset. We propose a new architecture for the GQ-CNN and describe practical improvements that increase the model validation accuracy from 92.2% to 95.8% and from 85.9% to 88.0% on respectively image-wise and object-wise training and validation splits.