Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational assessment of folding energy landscapes in heterodimeric coiled coils

The coiled coil structural motif consists of alpha helices supercoiling around each other to form staggered knobs‐into‐holes packing. Such structures are deceptively simple, especially as they often can be described with parametric equations, but are known to exist in various conformations. Even the simplest systems, consisting of 2 monomers, can assemble into a wide range of states. They can form canonical as well as noncanonical coiled coils, be parallel or antiparallel, where helices associate with different degrees of shift, tilt, and rotation. Here, we investigate the energy landscape of heterodimeric coiled coils by carrying out de novo folding simulations starting from amino acid sequence. We folded a diverse set of 22 heterodimers and demonstrate that the approach is capable of identifying the atomic details in the experimental structure in the majority of cases. Our methodology also enables exploration of alternative states that can be accessible in solution beyond the experimentally determined structure. For many systems, we observe folding energy landscapes with multiple energy minima and several isoenergetic states. By comparing coiled coils from single domains and those extracted from larger proteins, we find that standalone coiled coils have deeper energy wells at the experimentally determined conformation. By folding the competing homodimeric states in addition to the heterodimers, we observe that the structural specificity towards the heteromeric state is often small. Taken together, our results demonstrate that de novo folding simulations can be a powerful tool to characterize structural specificity of coiled coils when coupled to assessment of energy landscapes.
Dutch obesity intervention in teenagers: effectiveness of a school-based program on body composition and behavior.

OBJECTIVE To determine whether a multicomponent health promotion intervention for Dutch adolescents (defined as persons between 12 and 14 years of age) would be successful in influencing body composition and dietary and physical activity behavior in both the short and long terms. DESIGN Randomized controlled trial. SETTING Ten intervention and 8 control prevocational secondary schools. PARTICIPANTS A total of 1108 adolescents (mean age, 12.7 years). Intervention An interdisciplinary program with an adapted curriculum for 11 lessons in biology and physical education and environmental change options. MAIN OUTCOME MEASURES Body height and weight, waist circumference, 4 skinfold thickness measurements, and dietary and physical activity behavior data. RESULTS Multilevel analyses showed that the intervention remained effective in preventing unfavorable increases in important measures of body composition after 20-month follow-up in girls (biceps skinfold and sum of 4 skinfolds) and boys (triceps, biceps, and subscapular skinfolds). Consumption of sugar-containing beverages was significantly lower in intervention schools both after intervention (boys: -287 mL/d; 95% confidence interval [CI], -527 to -47; girls: -249; -400 to -98) and at 12-month follow-up (boys: -233; -371 to -95; girls: -271; -390 to -153). For boys, screen-viewing behavior was significantly lower in the intervention group after 20 months (-25 min/d; 95% CI, -50 to -0.3). No significant intervention effects on consumption of snacks or active commuting to school were found. CONCLUSION The Dutch Obesity Intervention in Teenagers program resulted in beneficial effects on the sum of skinfold thickness measurements in girls and consumption of sugar-containing beverages in both boys and girls in both the short and long terms.
Characterization of enzymatic glucose biosensor in buffer solution, in artificial saliva, and in potassium ferricyanide by linear sweep voltammetry

Existing practice of glucose-level monitoring for diabetic patients involves frequent finger pricking for blood samples. This is not only constantly painful, but could make patients susceptible to infections. A non-invasive, portable, graphene-based biosensor is being developed to measure glucose levels in saliva instead of in blood, by incorporating rGO-PEDOT:PSS composites as the transducer layer on a working electrode – a screen-printed carbon electrode (SPCE) 2 mm in diameter. To evaluate the performance of the biosensor, the electrochemical technique of linear sweep voltammetry (LSV) was used. The results showed sensitivity of rGO-PEDOT:PSS-GOx/SPCE in artificial saliva: 105 μA/mM (σ = 12.52) at no glucose to 0.2 mM glucose concentrations and 35.33 μA/mM (σ = 5.79) at glucose concentrations of 0.2 mM to 0.6 mM, with correlation coefficient of 0.99. The sensitivity of the biosensor in 10 mM PBS (pH 6.8) is 9.88 μA/mM (σ = 2.74), while in 100 mM potassium ferricyanide it is 10.48 μA/mM (σ = 0.49). The high sensitivity obtained in artificial saliva suggests that the rGO-PEDOT:PSS composite is suitable for use as a transducer layer for non-invasive glucose monitoring.
Virtual Cells and Virtual Networks Enablelow-Latency Vehicle-to-Vehicle Communication

This paper presents a framework for pursuing lowlatency communication among V2V networks underlaying V2I networks. To achieve low-latency communication, solely relying on the improvement of the air-interface may not be enough. To cope with the highly dynamic environment of vehicular networks, a time dynamic optimization approach is proposed that improves the latency performance through not only optimization of spectrum resources but also by constraining the network switching rate. To further decrease the complexity of the time dynamic optimization problem, we convert the original problem to a deterministic optimization problem through the Lyapunov Optimization Theory. The proposed algorithm becomes a more suitable scheme for the vehicular network. Analytical results show that the proposed scheme can approach the best tradeoff between the latency performance and the network switching rate. Simulation results are provided to verify the proposed algorithm.
CoNet: Collaborative Cross Networks for Cross-Domain Recommendation

The cross-domain recommendation technique is an effective way of alleviating the data sparse issue in recommender systems by leveraging the knowledge from relevant domains. Transfer learning is a class of algorithms underlying these techniques. In this paper, we propose a novel transfer learning approach for cross-domain recommendation by using neural networks as the base model. In contrast to the matrix factorization based cross-domain techniques, our method is deep transfer learning, which can learn complex user-item interaction relationships. We assume that hidden layers in two base networks are connected by cross mappings, leading to the collaborative cross networks (CoNet). CoNet enables dual knowledge transfer across domains by introducing cross connections from one base network to another and vice versa. CoNet is achieved in multi-layer feedforward networks by adding dual connections and joint loss functions, which can be trained efficiently by back-propagation. The proposed model is thoroughly evaluated on two large real-world datasets. It outperforms baselines by relative improvements of 7.84% in NDCG. We demonstrate the necessity of adaptively selecting representations to transfer. Our model can reduce tens of thousands training examples comparing with non-transfer methods and still has the competitive performance with them.
En bloc vertebrectomy for the treatment of spinal lesions. Five years of experience in a single institution: a case series

OBJECTIVES: The objective of this study is to describe the experience of a Brazilian public university hospital regarding the treatment of metastatic or benign spine lesions with en bloc vertebrectomy of the thoracic and lumbar spines. METHODS: This study was a retrospective case series and included all medical records of patients with benign aggressive, primary malignant, or metastatic spine lesions who underwent en bloc vertebrectomy from 2010 to 2015. RESULTS: A total of 17 patients were included in the analysis. Most of them (71%) were indicated for surgery based on an oncologic resection for localized disease cure. Overall, 10 of the 17 patients (59%) underwent vertebrectomy via an isolated posterior approach using the technique described by Roy-Camille et al. and Tomita et al., while 7 patients (41%) underwent double approach surgeries. Of the 17 patients who underwent the en bloc resection, 8 are still alive and in the outpatient follow-up (47%), and almost all patients with metastatic lesions (8/9) died. The average survival time following the surgical procedure was 23.8 months. Considering the cases of metastatic lesions and the cases of localized disease (malignant or benign aggressive disease) separately, we observed an average survival time of 15 months and 47.6 months respectively. CONCLUSION: This study demonstrates and reinforces the reproducibility of the en bloc vertebrectomy technique described by Tomita et al.
Metabotropic glutamate receptors as a new therapeutic target for malignant gliomas

Metabotropic glutamate receptors (mGluR) are predominantly involved in maintenance of cellular homeostasis of central nervous system. However, evidences have suggested other roles of mGluR in human tumors. Aberrant mGluR signaling has been shown to participate in transformation and maintenance of various cancer types, including malignant brain tumors. This review intends to summarize recent findings regarding the involvement of mGluR-mediated intracellular signaling pathways in progression, aggressiveness, and recurrence of malignant gliomas, mainly glioblastomas (GBM), highlighting the potential therapeutic applications of mGluR ligands. In addition to the growing number of studies reporting mGluR gene or protein expression in glioma samples (resections, lineages, and primary cultures), pharmacological blockade in vitro of mGluR1 and mGluR3 by selective ligands has been shown to be anti-proliferative and anti-migratory, decreasing activation of MAPK and PI3K pathways. In addition, mGluR3 antagonists promoted astroglial differentiation of GBM cells and also enabled cytotoxic action of temozolomide (TMZ). mGluR3-dependent TMZ toxicity was supported by increasing levels of MGMT transcripts through an intracellular signaling pathway that sequentially involves PI3K and NF-? B. Further, continuous pharmacological blockade of mGluR1 and mGluR3 have been shown to reduced growth of GBM tumor in two independent in vivo xenograft models. In parallel, low levels of mGluR3 mRNA in GBM resections may be a predictor for long survival rate of patients. Since several Phase I, II and III clinical trials are being performed using group I and II mGluR modulators, there is a strong scientifically-based rationale for testing mGluR antagonists as an adjuvant therapy for malignant brain tumors.
Report of a workshop on ensuring sustainable access to safe blood in developing countries: International Blood Safety Forum, March 24, 2017

On March 24, 2017, more than 90 experts in blood safety and international development from blood centers, industry, government, and international and nongovernmental organizations gathered in Arlington, Virginia, for the Third International Blood Safety Forum, cosponsored by America's Blood Centers and Global Healing. This report summarizes presentations and major conclusions. The meeting explored ways to increase access to affordable, safe blood for low‐ and lower‐middle‐income countries (LMICs) in an era when funding from the US President's Emergency Plan for AIDS Relief (PEPFAR) and the Global Fund has been redirected from preventing the spread of human immunodeficiency virus (HIV) to diagnosing and treating the 25 million‐plus people living with HIV in LMICs. More effective management systems must be developed to improve cost recovery for blood. While blood systems become more sustainable, continued investment is required to keep them operating. The traditional model of large grants from bilateral and multilateral donors will need to be supplemented (or replaced) with public‐private partnerships and nongovernmental investment. A continued emphasis on quality is fundamental. Blood systems must build quality programs, based on accepted standards, including hospitals, clinics, and rural health care providers to ensure proper and safe use of blood. Proposals to resolve health care inequities between LMICs and high‐income countries (HICs) must include helping LMICs to define sustainable national policies and practices for blood availability and utilization to suit local contexts. The blood safety lexicon should be revised to include availability, accessibility, and affordability of safe blood and blood products as the goal of all blood safety initiatives.
RESDORE : Robust Estimation in Spherical Deconvolution by Outlier Rejection

Purpose Corrupted diffusion-weighted (DW) signals can have pronounced negative effects on derived indices [1]. One solution, RESTORE, [1,2] is to exclude corrupted signals from the tensor model fitting processes. Taking inspiration from this approach, we have developed a novel pipeline that extends the principle to robust recovery of the fibre orientation distribution functions (fODF) in spherical deconvolution methods. RESDORE (Robust Estimation in Spherical Deconvolution by Outlier REjection) detects outliers as non-axially symmetric signal components, and rejects them improving the fit and recovery of fODF .
Benefits of spiral imaging for Arterial Spin Labeling as compared to EPI

Audience: RF engineers and MR physicists. Purpose: Different imaging methods can be used for pulsed arterial spin labeling (PASL). Often, single-shot 2D echo planar imaging (EPI) is used with PASL techniques, since it is fast at a reasonable resolution. In this study, the PICORE PASL method with Q2TIPS saturation is evaluated with different imaging modules: blipped EPI (bEPI) with different partial-Fourier sampling and spiral EPI (sEPI) with different no. of segments. Shorter readout with partial-Fourier or segmentation can decrease the echo time and thus be beneficial for signal-to-noise ratio (SNR) and image quality by reducing off-resonance distortions. On the other hand, resolution may be sacrificed and physiologically induced segmentation artifacts and subject motion may counteract and dampen the advantages. The comparison of blipped and spiral EPI images itself is not straightforward since different point-spread functions show principally different artifact appearances, like phase-encode shifts for bEPI and radial blurring for sEPI. The goal of this study was to acquire human PASL data at 3T with the different imaging modules to compare the best ASL quality in terms of SNR and the least artifact levels.
Canonical Consistent Weighted Sampling for Real-Value Weighted Min-Hash

Min-Hash, as a member of the Locality Sensitive Hashing (LSH) family for sketching sets, plays an important role in the big data era. It is widely used for efficiently estimating similarities of bag-of-words represented data and has been extended to dealing with multi-sets and real-value weighted sets. Improved Consistent Weighted Sampling (ICWS) has been recognized as the state-of-the-art for real-value weighted Min-Hash. However, the algorithmic implementation of ICWS is flawed because it violates the uniformity of the Min-Hash scheme. In this paper, we propose a Canonical Consistent Weighted Sampling (CCWS) algorithm, which not only retains the same theoretical complexity as ICWS but also strictly complies with the definition of Min-Hash. The experimental results demonstrate that the proposed CCWS algorithm runs faster than the state-of-the-arts while achieving similar classification performance on a number of real-world text data sets.
Experimental investigation of fan-folded piezoelectric energy harvesters for powering pacemakers

This paper studies the fabrication and testing of a magnet free piezoelectric energy harvester (EH) for powering biomedical devices and sensors inside the body. The design for the EH is a fan-folded structure consisting of bimorph piezoelectric beams folding on top of each other. An actual size experimental prototype is fabricated to verify the developed analytical models. The model is verified by matching the analytical results of the tip acceleration frequency response functions (FRF) and voltage FRF with the experimental results. The generated electricity is measured when the EH is excited by the heartbeat. A closed loop shaker system is utilized to reproduce the heartbeat vibrations. Achieving low fundamental natural frequency is a key factor to generate sufficient energy for pacemakers using heartbeat vibrations. It is shown that the natural frequency of the small-scale device is less than 20 Hz due to its unique fan-folded design. The experimental results show that the small-scale EH generates sufficient power for state of the art pacemakers. The 1 cm3 EH with 18.4 g r tip mass generates more than 16 μ W of power from a normal heartbeat waveform. The robustness of the device to the heart rate is also studied by measuring the relation between the power output and the heart rate.
Predicting Reading and Mathematics From Neural Activity for Feedback Learning

Although many studies use feedback learning paradigms to study the process of learning in laboratory settings, little is known about their relevance for real-world learning settings such as school. In a large developmental sample (N = 228, 8–25 years), we investigated whether performance and neural activity during a feedback learning task predicted reading and mathematics performance 2 years later. The results indicated that feedback learning performance predicted both reading and mathematics performance. Activity during feedback learning in left superior dorsolateral prefrontal cortex (DLPFC) predicted reading performance, whereas activity in presupplementary motor area/anterior cingulate cortex (pre-SMA/ACC) predicted mathematical performance. Moreover, left superior DLPFC and pre-SMA/ACC activity predicted unique variance in reading and mathematics ability over behavioral testing of feedback learning performance alone. These results provide valuable insights into the relationship between laboratory-based learning tasks and learning in school settings, and the value of neural assessments for prediction of school performance over behavioral testing alone.
Oculomotor Status, Binocular Vision, and Stereoacuity in a Series of Keratoconus Subjects.

Purpose A group of keratoconus subjects (KG) and a control group (CG) were evaluated for sensory and motor status. We tried to clarify the factors (best-corrected visual acuity [BCVA]), heterophorias, fusional amplitude, anisometropia, astigmatism) that may be associated with a binocular disturbance. Methods BCVA (logMAR) was measured. Binocular vision was checked using cover tests, striate Maddox, and a 6Δ base-down prism (simultaneous perception), a prism bar (fusion and fusional convergence break point), and Titmus Fly Test (stereopsis). Results Fifty-four subjects of the KG, 27 men (median 16 years), and 29 of the CG, 15 men (median 20 years), were evaluated. In the KG, 8 (15%) subjects had strabismus. Those whose BCVA in the worse eye was logMAR ≥0.7 had a significantly higher frequency of strabismus and absence of simultaneous perception. Spherical equivalent anisometropia ≥ 1.0 diopter (D) was significantly different in both groups as was the frequency of gross stereopsis. In comparing fine and gross stereopsis in both the KG and the CG, there was a significant difference in the frontal astigmatism between eyes in the KG (P = 0.03) and CG (P = 0.01). Conclusions In our study, the KG presented a higher frequency of strabismus and impaired binocular vision. Frontal astigmatism was different between groups with gross and fine stereopsis, in both the CG and KG. Future studies are needed to elucidate or reinforce the factors associated with the loss of binocularity in keratoconus. Testing for stereopsis may be helpful to consider in the treatment guidelines for keratoconus.
Transmission electron microscopy and spectroscopy of carbon-based nanomaterials

Faculty of Engineering, Mathematics and Science School of Chemistry Doctor of Philosophy Transmission Electron Microscopy and Spectroscopy of Carbon-based Nanomaterials by Ehsan Rezvani Carbon-based nanomaterials, such as graphene, Carbon Nanotubes and fullerenes, have attracted a great deal of interest from the materials research community; especially in electronic and sensing applications. Despite all these outstanding properties, these materials pose significant challenges to the established characterisation techniques. Transmission electron microscopy (TEM) is considered as a powerful tool to tackle this challenge due to its capability to achieve images of atomic-scale resolution. Nonetheless, a key requirement for efficient application of TEM, is sample quality. To meet this need, in the first part of this work, modification of the CVD growth of graphene via catalyst optimisation was investigated and is reported in a dedicated chapter. We show that chromium can be used to successfully obtain entirely monolayer graphene films. The second part of this study, comprises HRTEM/EELS investigation of plasma-functionalised graphene; where we propose application of these two methods as a tool to monitor the quality of plasma-treated graphene sheets. We then move on to explore the bonding properties of isotope-enriched graphene studied by Aberration-Corrected TEM. The results show that the bonds in isotope graphene are stronger and remarkably longer comparing to those of “normal” graphene.
Formulation and evaluation of controlled-release of steroidal saponins-loaded collagen microspheres

ABSTRACT The purpose of this study was to develop a collagen (COL) microspheres-based steroidal saponin (SS) formulation which was expected to sustain release of SS with high encapsulation efficiency. The microspheres were prepared by water-in-oil-in water double-emulsion solvent evaporation technique with different formulation variables such as concentration of COL and emulsification time. The optimised SS microspheres were prepared successfully with average diameter of 8.68 ± 0.34 μm, encapsulation efficiency up to 67.63 ± 1.31%, and integrated spherical shape with no drug crystal and porous on its surface. The in-vitro drug release studies showed marked retardation of SS release and higher percentage of COL gave longer drug release profile. Higuchi model was found to be the best fitted for drug release from COL microspheres of all formulations. This may suggest the potential use of SS microspheres for treatment of bone tissue engineering over long periods.
A Lattice Basis Reduction Approach for the Design of Finite Wordlength FIR Filters

Many applications of finite impulse response (FIR) digital filters impose strict format constraints on the filter coefficients. Such requirements increase the complexity of determining optimal designs for the problem at hand. We introduce a fast and efficient method, based on the computation of good nodes for polynomial interpolation and Euclidean lattice basis reduction. Experiments show that it returns quasi-optimal finite wordlength FIR filters; compared to previous approaches it also scales remarkably well (length 125 filters are treated in $<$ 9 s). It also proves useful for accelerating the determination of optimal finite wordlength FIR filters.