Miracle-dz/UniFAR-FTUs huggingface dataset:
A disciplined approach to neural network hyper-parameters: Part 1 - learning rate, batch size, momentum, and weight decay

Although deep learning has produced dazzling successes for applications of image, speech, and video processing in the past few years, most trainings are with suboptimal hyper-parameters, requiring unnecessarily long training times. Setting the hyper-parameters remains a black art that requires years of experience to acquire. This report proposes several efficient ways to set the hyper-parameters that significantly reduce training time and improves performance. Specifically, this report shows how to examine the training validation/test loss function for subtle clues of underfitting and overfitting and suggests guidelines for moving toward the optimal balance point. Then it discusses how to increase/decrease the learning rate/momentum to speed up training. Our experiments show that it is crucial to balance every manner of regularization for each dataset and architecture. Weight decay is used as a sample regularizer to show how its optimal value is tightly coupled with the learning rates and momentums. Files to help replicate the results reported here are available.
Finding the edge: Art and automation

I first fell in love with computer programming through the lens of art. Although I had a brief introduction through an undergraduate programming class, the first exposure that really hooked me was a course called “Programming for Artists. ” Like many artists before me, using code for art creation opened powerful new forms of expression. Programming allowed for the creation of interactive pieces that changed depending on the behavior of the people viewing them. I also learned how artists could write programs that autonomously made artistic decisions and produced generative works. Eventually, I started to understand
Embedded atom calculations of unstable stacking fault energies and surface energies in intermetallics

We performed embedded atom method calculations of surface energies and unstable stacking fault energies for a series of intermetallics for which interatomic potentials of the embedded atom type have recently been developed. These results were analyzed and applied to the prediction of relative ductility of these materials using the various current theories. Series of alloys with the B2 ordered structure were studied, and the results were compared to those in pure body-centered cubic (bcc) Fe. Ordered compounds with L 1_2 and L 1_0 structures based on the face-centered cubic (fcc) lattice were also studied. It was found that there is a correlation between the values of the antiphase boundary (APB) energies in B2 alloys and their unstable stacking fault energies. Materials with higher APB energies tend to have higher unstable stacking fault energies, leading to an increased tendency to brittle fracture.
Evaluation of Biometric Template Protection Schemes based on a Transformation

With more and more applications using biometrics, new privacy and security risks arise. New biometric schemes have been proposed in the last decade following a privacy by design approach: biometric template protection systems. Their quantitative evaluation is still an open research issue. The objective of this paper is to propose a new evaluation methodology for template protection systems based on a transformation by proposing some metrics for testing their performance and robustness to face attacks. These metrics enable us to estimate the probability of successful attacks considering different scenarios. We illustrate this evaluation methodology on two transformation based template protection schemes in order to show how some security and privacy properties can be checked by simulating attacks.
Brain–computer interfaces as new brain output pathways

Brain–computer interfaces (BCIs) can provide non‐muscular communication and control for people with severe motor disabilities. Current BCIs use a variety of invasive and non‐invasive methods to record brain signals and a variety of signal processing methods. Whatever the recording and processing methods used, BCI performance (e.g. the ability of a BCI to control movement of a computer cursor) is highly variable and, by the standards applied to neuromuscular control, could be described as ataxic. In an effort to understand this imperfection, this paper discusses the relevance of two principles that underlie the brain's normal motor outputs. The first principle is that motor outputs are normally produced by the combined activity of many CNS areas, from the cortex to the spinal cord. Together, these areas produce appropriate control of the spinal motoneurons that activate muscles. The second principle is that the acquisition and life‐long preservation of motor skills depends on continual adaptive plasticity throughout the CNS. This plasticity optimizes the control of spinal motoneurons. In the light of these two principles, a BCI may be viewed as a system that changes the outcome of CNS activity from control of spinal motoneurons to, instead, control of the cortical (or other) area whose signals are used by the BCI to determine the user's intent. In essence, a BCI attempts to assign to cortical neurons the role normally performed by spinal motoneurons. Thus, a BCI requires that the many CNS areas involved in producing normal motor actions change their roles so as to optimize the control of cortical neurons rather than spinal motoneurons. The disconcerting variability of BCI performance may stem in large part from the challenge presented by the need for this unnatural adaptation. This difficulty might be reduced, and BCI development might thereby benefit, by adopting a ‘goal‐selection’ rather than a ‘process‐ control’ strategy. In ‘process control’, a BCI manages all the intricate high‐speed interactions involved in movement. In ‘goal selection’, by contrast, the BCI simply communicates the user's goal to software that handles the high–speed interactions needed to achieve the goal. Not only is ‘goal selection’ less demanding, but also, by delegating lower‐level aspects of motor control to another structure (rather than requiring that the cortex do everything), it more closely resembles the distributed operation characteristic of normal motor control.
bFGF promotes Sca-1+ cardiac stem cell migration through activation of the PI3K/Akt pathway

Cardiac stem cells (CSCs) are important for improving cardiac function following myocardial infarction, with CSC migration to infarcted or ischemic myocardium important for cardiac regeneration. Strategies to improve cell migration may improve the efficiency of myocardial regeneration. Basic fibroblast growth factor (bFGF) is an essential molecule in cell migration, but the endogenous bFGF level is too low to be effective. The effect of exogenously delivered bFGF on CSC migration was observed in vitro and in vivo in the present study. The CSC migration index in response to various bFGF concentrations was demonstrated in vitro. In addition, a murine myocardial infarction model was constructed and bFGF protein expression levels and CSC aggregation following myocardial infarction were observed. To study cell migration in vivo, CM-Dil-labeled CSCs or bFGF-CSCs were injected into the peri-infarct myocardium following myocardium infarction and cell migration and maintenance in the peri-infarct/infarct area was observed 1 week later. Protein expression levels of bFGF, CXCR-4 and SDF-1 were assessed, as was myocardium capillary density. The Akt inhibitor deguelin was used to assess the role of the PI3K/Akt pathway in vitro and in vivo. The present study demonstrated that bFGF-promoted Sca-1+ CSC migration, with the highest migration rate occurring at a concentration of 45 ng/ml. The PI3K/Akt pathway inhibitor deguelin attenuated this increase. The phospho-Akt/Akt ratio was elevated significantly after 30 min of bFGF exposure. Transplantation of bFGF-treated Sca-1+ CSCs led to improved cell maintenance in the peri-infarct area and increased cell migration to the infarct area, as well as improved angiogenesis. Protein expression levels of bFGF, CXCR-4 and SDF-1 were upregulated, and this upregulation was partially attenuated by deguelin. Therefore, bFGF was demonstrated to promote Sca-1+ CSC migration both in vitro and in vivo, partially through activation of the PI3K/Akt pathway. This may provide a new method for facilitating CSC therapy for myocardium repair after myocardium injury.
Reverse Methanogenesis and Respiration in Methanotrophic Archaea

Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types.
Health facility management and access: a qualitative analysis of challenges to seeking healthcare for children under five in Uganda

Abstract While several studies have documented the various barriers that caretakers of children under five routinely confront when seeking healthcare in Uganda, few have sought to capture the ways in which caretakers themselves prioritize their own barriers to seeking services. To that end, we asked focus groups of caretakers to list their five greatest challenges to seeking care on behalf of children under five. Using qualitative content analysis, we grouped responses according to four categories: (1) geographical access barriers; (2) facility supplies, staffing, and infrastructural barriers; (3) facility management and administration barriers (e.g. health worker professionalism, absenteeism and customer care); and (4) household barriers related to financial circumstances, domestic conflicts with male partners and a stated lack of knowledge about health‐related issues. Among all focus groups, caretakers mentioned supplies, staffing and infrastructure barriers most often and facility management and administration barriers the least. Caretakers living furthest from public facilities (8‐10 km) more commonly mentioned geographical barriers to care and barriers related to financial and other personal circumstances. Caretakers who lived closest to health facilities mentioned facility management and administration barriers twice as often as those who lived further away. While targeting managerial barriers is vitally important—and increasingly popular among national planners and donors‐it should be done while recognizing that alleviating such barriers may have a more muted effect on caretakers who are geographically harder to reach ‐ and by extension, those whose children have an increased risk of mortality. In light of calls for greater equity in child survival programming ‐ and given the limited resource envelopes that policymakers often have at their disposal ‐ attention to the barriers considered most vital among caretakers in different settings should be weighed.
Effects of dignity therapy on terminally ill patients: a systematic review.

OBJECTIVE Analyzing the evidence of the effects of dignity therapy onterminally ill patients. METHOD A Systematic review of the literature conducted using the search strategy in six databases. Inclusion criteria were primary studies, excluding literature reviews (systematic or not) and conceptual articles. RESULTS Ten articles were analyzed regarding method, results and evidence level. Dignity therapy improved the sense of meaning andpurpose, will to live, utility, quality of life, dignity and family appreciationin studies with a higher level of evidence. The effects are not well established in relation to depression, anxiety, spirituality and physical symptoms. CONCLUSION Studies with a moderate to high level of evidence have shown increased sense of dignity, will to live and sense of purpose. Further studies should be developed to increase knowledge about dignity therapy. OBJETIVO Analisar as evidências sobre os efeitos da terapia da dignidade para pacientes em fase terminal de vida. MÉTODO Revisão sistemática da literatura realizada em seis bases de dados na estratégia de busca. Os critérios de inclusão foram estudos primários, excluindo-se revisões da literatura (sistemáticas ou não) e artigos conceituais. RESULTADOS Dez artigos foram analisados quanto ao método, aos resultados e nível de evidência. Nos estudos com maior nível de evidência, a terapia da dignidade melhorou o senso de significado, propósito, vontade de viver, utilidade, qualidade de vida, dignidade e apreciação familiar.Os efeitos não estão bem estabelecidos em relação à depressão, ansiedade, espiritualidade e aos sintomas físicos. CONCLUSÃO Os estudos de nível de evidência de moderado a alto demonstraram aumento do senso de dignidade, vontade de viver e senso de propósito. Mais estudos devem ser desenvolvidos para ampliar o conhecimento sobre a terapia da dignidade.
The feasibility of conducting a randomised controlled trial comparing arthroscopic hip surgery to conservative care for patients with femoroacetabular impingement syndrome: the FASHIoN feasibility study

To determine whether it was feasible to perform a randomized controlled trial (RCT) comparing arthroscopic hip surgery to conservative care in patients with femoroacetabular impingement (FAI). This study had two phases: a pre-pilot and pilot RCT. In the pre-pilot, we conducted interviews with clinicians who treated FAI and with FAI patients to determine their views about an RCT. We developed protocols for operative and conservative care. In the pilot RCT, we determined the rates of patient eligibility, recruitment and retention, to investigate the feasibility of the protocol and we established methods to assess treatment fidelity. In the pre-pilot phase, 32 clinicians were interviewed, of which 26 reported theoretical equipoise, but in example scenarios 7 failed to show clinical equipoise. Eighteen patients treated for FAI were also interviewed, the majority of whom felt that surgery and conservative care were acceptable treatments. Surgery was viewed by patients as a ‘definitive solution’. Patients were motivated to participate in research but were uncomfortable about randomization. Randomization was more acceptable if the alternative was available at the end of the trial. In the pilot phase, 151 patients were assessed for eligibility. Sixty were eligible and invited to take part in the pilot RCT; 42 consented to randomization. Follow-up was 100% at 12 months. Assessments of treatment fidelity were satisfactory. An RCT to compare arthroscopic hip surgery with conservative care in patients with FAI is challenging but feasible. Recruitment has started for a full RCT.
Pedestrian and Bicyclist Identification Through Micro Doppler Signature With Different Approaching Aspect Angles

In realistic road scenarios, two main urban hazards, pedestrians and bicyclists, can approach the radar from any aspect angle which will affect the ability of a radar system to perform target identification. However, the identification of these two particular types of targets with different approaching directions has not been investigated thoroughly until now. In this paper, we explore the micro Doppler signature to accurately distinguish pedestrian and the bicyclist. One feature extraction method that is based on the sparse coding of a measured micro Doppler signature is proposed and validated. Further numerical analysis of the sparse matrices was performed to reduce the number of dimensions whilst keeping a sufficient number of features. As on comparison, the two feature extractors, i.e., singular value decomposition and robust principal component analysis are extensively studied and compared with the proposed method. Support vector machine (SVM) and extreme learning machine were adopted to classify the extracted features. Indoor experimental results indicate that the proposed methods can achieve higher identification accuracies than alternative approaches and the outdoor measurement results presented show good performance with realistic targets.
Metagenomic potential for and diversity of N‐cycle driving microorganisms in the Bothnian Sea sediment

The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)‐based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N2, but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR‐based technique. The results reveal the importance of various N‐cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.
Portion size and later food intake: evidence on the "normalizing" effect of reducing food portion sizes.

Background Historical increases in the size of commercially available food products have been linked to the emergence of a worldwide obesity crisis. Although the acute effect that portion size has on food intake is well established, the effect that exposure to smaller portion sizes has on future portion size selection has not been examined. Objective We tested whether reducing a food portion size "renormalizes" perceptions of what constitutes a normal amount of that food to eat and results in people selecting and consuming smaller portions of that food in the future. Design Across 3 experiments, participants were served a larger or smaller portion of food. In experiments 1 and 2, participants selected and consumed a portion of that food 24 h later. In experiment 3, participants reported on their preferred ideal portion size of that food after 1 wk. Results The consumption of a smaller, as opposed to a larger, portion size of a food resulted in participants believing a "normal"-sized portion was smaller (experiments 1-3, P ≤ 0.001), consuming less of that food 1 d later (experiments 1-2, P ≤ 0.003), and displaying a tendency toward choosing a smaller ideal portion of that food 1 wk later (experiment 3, P = 0.07), although the latter finding was not significant. Conclusion Because consumer preferences appear to be driven by environmental influences, reducing food portion sizes may recalibrate perceptions of what constitutes a "normal" amount of food to eat and, in doing so, decrease how much consumers choose to eat. This trial was registered at www.clinicaltrials. gov as NCT03241576.
Treadmill training after spinal cord injury

The editorial by Dr. Wolpaw highlights the significance of the first multi-randomized clinical trial (MCRCT) for neurorehabilitation after acute spinal cord injury (SCI). 1 Several therapeutic implications of the trial that were not addressed warrant discussion. In this trial, the effect of body weight supported treadmill training (BWSTT) was compared to a control overground mobility training (CONT), not to conventional rehabilitation for individuals with incomplete SCI. A large sample of people with typical ASIA B, C, and D injuries received standing and gait training. The experimental arm received BWSTT followed by immediate practice overground. Training afforded the sensory-specific experience of walking and emphasized weight-bearing on the legs. The control group received overground standing and usual gait training. Both groups received 40 to 60 training sessions, a higher frequency than is typically provided. The MCRCT demonstrated for the first time that ASIA C and D subjects in both groups achieved significant gains 6 months after study entry. Most subjects attained abilities sufficient for community ambulation including a fast speed (1.0 m/s), relatively good endurance (400 m in 6 min) without walking aids, and excellent balance (54/56 Berg balance). Therefore, the trial demonstrates that aggressive rehabilitation in the early phase of SCI is likely to benefit a very high percentage of these individuals. Specifically, these results suggest that at least one h/day of weight-bearing standing and gait training should be emphasized as early as possible for up to 60 sessions, likely resulting in a progressive increase in walking speed over time, but this relationship requires further investigation. The findings of the current clinical trial now set the minimum recovery standards by which all …
Differential Expression Levels of Integrin α6 Enable the Selective Identification and Isolation of Atrial and Ventricular Cardiomyocytes

Rationale Central questions such as cardiomyocyte subtype emergence during cardiogenesis or the availability of cardiomyocyte subtypes for cell replacement therapy require selective identification and purification of atrial and ventricular cardiomyocytes. However, current methodologies do not allow for a transgene-free selective isolation of atrial or ventricular cardiomyocytes due to the lack of subtype specific cell surface markers. Methods and Results In order to develop cell surface marker-based isolation procedures for cardiomyocyte subtypes, we performed an antibody-based screening on embryonic mouse hearts. Our data indicate that atrial and ventricular cardiomyocytes are characterized by differential expression of integrin α6 (ITGA6) throughout development and in the adult heart. We discovered that the expression level of this surface marker correlates with the intracellular subtype-specific expression of MLC-2a and MLC-2v on the single cell level and thereby enables the discrimination of cardiomyocyte subtypes by flow cytometry. Based on the differential expression of ITGA6 in atria and ventricles during cardiogenesis, we developed purification protocols for atrial and ventricular cardiomyocytes from mouse hearts. Atrial and ventricular identities of sorted cells were confirmed by expression profiling and patch clamp analysis. Conclusion Here, we introduce a non-genetic, antibody-based approach to specifically isolate highly pure and viable atrial and ventricular cardiomyocytes from mouse hearts of various developmental stages. This will facilitate in-depth characterization of the individual cellular subsets and support translational research applications.