Miracle-dz/UniFAR-FTUs huggingface dataset:
The hunt for the most-wanted chemolithoautotrophic spookmicrobes

ABSTRACT Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic ‘Candidatus Methanothrix paradoxum’, which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, ‘Candidatus Methanoperedens nitroreducens’ ANME-2d archaea and ‘Candidatus Methylomirabilis oxyfera’ bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although ‘Candidatus Methanoperedens nitroreducens’ and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.
Great tits and the city: Distribution of genomic diversity and gene–environment associations along an urbanization gradient

Urbanization is a growing concern challenging the evolutionary potential of wild populations by reducing genetic diversity and imposing new selection regimes affecting many key fitness traits. However, genomic footprints of urbanization have received little attention so far. Using RAD sequencing, we investigated the genomewide effects of urbanization on neutral and adaptive genomic diversity in 140 adult great tits Parus major collected in locations with contrasted urbanization levels (from a natural forest to highly urbanized areas of a city; Montpellier, France). Heterozygosity was slightly lower in the more urbanized sites compared to the more rural ones. Low but significant effect of urbanization on genetic differentiation was found, at the site level but not at the nest level, indicative of the geographic scale of urbanization impact and of the potential for local adaptation despite gene flow. Gene–environment association tests identified numerous SNPs with small association scores to urbanization, distributed across the genome, from which a subset of 97 SNPs explained up to 81% of the variance in urbanization, overall suggesting a polygenic response to selection in the urban environment. These findings open stimulating perspectives for broader applications of high‐resolution genomic tools on other cities and larger sample sizes to investigate the consistency of the effects of urbanization on the spatial distribution of genetic diversity and the polygenic nature of gene–urbanization association.
Fairness-oriented resource allocation for energy efficiency optimization in uplink OFDMA networks

Due to the battery-limited nature of mobile devices, improving energy efficiency (EE) of individual users and ensuring EE fairness among those users are one of the key design issues in uplink transmission of cellular networks. In this paper, we consider the joint optimization of discrete power and resource blocks allocations to maximize the minimum EE among users subject to individual power budget constraints. The optimization problem is combinatorial. Thus, we propose an efficient algorithm, based on semidefinite relaxation with Gaussian randomization, to solve the resultant non-convex problem in polynomial time complexity. The numerical results show how well the proposed algorithm performs against the optimal one and indicate the impact of discrete power levels on the fairness-oriented EE optimization.
Preoperative Use of a 3D Printed Model for Femoroacetabular Impingement Surgery and Its Effect on Planned Osteoplasty.

OBJECTIVE The purpose of this study was to determine the effect that preoperative use of 3D printed models has on planned osteoplasty for femoroacetabular impingement (FAI) surgery. MATERIALS AND METHODS This experimental study utilizing retrospective data included 10 consecutive patients from July 1, 2013, to January 1, 2015, with a clinical diagnosis of FAI and imaging consisting of radiographs, CT scans, and MR images. Three-dimensional models of each patient's affected hip were printed to scale from CT data. Two orthopedic surgeons evaluated each patient in a routine preoperative manner. The effect of the 3D models in altering the planned osteoplasty was then determined. Proportions of osteoplasty change were calculated at various positions, and categoric variables were assessed with the chi-square test for independence. RESULTS Proportions of osteoplasty changes ranged from 20% to 55% at femoral positions (greatest at lateral and depth positions) and 35-75% at acetabular positions (greatest at anterior and depth positions). More osteoplasty changes occurred in patients with alpha angles of 60° or more (p = 0.00030) and without a radiographic crossover sign (p = 0.0075). We found no difference in the proportion of osteoplasty changes when stratifying by lateral center edge angle and coxa profunda (p = 0.190 and 0.109, respectively). The planned osteoplasty was changed for at least one reader in 9/10 (90%) femurs and 10/10 (100%) acetabula. CONCLUSION Use of 3D models in preoperative planning can change both the extent and location of planned osteoplasty for FAI surgery and is particularly influential in patients with alpha angles of 60° or more and without a radiographic crossover.
Extended Diffix

A longstanding open problem is that of how to get high quality statistics through direct queries to databases containing information about individuals without revealing information specific to those individuals. Diffix is a new framework for anonymous database query that adds noise based on the filter conditions in the query. A previous paper described Diffix for a simplified query semantics. This paper extends that description to include a wide variety of common features found in SQL. It describes attacks associated with various features, and the anonymization steps used to defend against those attacks. This paper describes the version of Diffix used for bounty program sponsored by Aircloak starting December 2017.
Inferring the Intentions of Learning Agents

This thesis addresses the problem of inferring the goals, represented as a utility function, of an intelligent agent who is learning in a known way. It generalizes the standard inverse reinforcement learning (IRL) problem, where it is assumed that the agent does not (need to) learn and makes decisions optimally. Here, it is assumed instead that the agent may learn in a known way and makes decisions in a known, albeit not necessarily optimal, way. In addition to laying out the general problem, I identify two of its special cases and solve them with polynomial-time algorithms. One formulates the problem as a linear program, and the other formulates the problem as one of maximum a posteriori estimation and uses a gradient descent approach that is guaranteed to converge.
Reduced-Order Modeling through Machine Learning Approaches for Brittle Fracture Applications

In this paper, five different approaches for reduced-order modeling of brittle fracture in geomaterials, specifically concrete, are presented and compared. Four of the five methods rely on machine learning (ML) algorithms to approximate important aspects of the brittle fracture problem. In addition to the ML algorithms, each method incorporates different physics-based assumptions in order to reduce the computational complexity while maintaining the physics as much as possible. This work specifically focuses on using the ML approaches to model a 2D concrete sample under low strain rate pure tensile loading conditions with 20 preexisting cracks present. A high-fidelity finite element-discrete element model is used to both produce a training dataset of 150 simulations and an additional 35 simulations for validation. Results from the ML approaches are directly compared against the results from the high-fidelity model. Strengths and weaknesses of each approach are discussed and the most important conclusion is that a combination of physics-informed and data-driven features are necessary for emulating the physics of crack propagation, interaction and coalescence. All of the models presented here have runtimes that are orders of magnitude faster than the original high-fidelity model and pave the path for developing accurate reduced order models that could be used to inform larger length-scale models with important sub-scale physics that often cannot be accounted for due to computational cost.
Unusual Signs and Symptoms in HIV-Positive Patients Coinfected with Leishmania spp: The Importance of Neglected Tropical Disease in Differential Diagnosis

BACKGROUND: Leishmaniasis is a parasitic disease affecting both animals and humans, acquired with the bite of sand flies or, in Injection Drug Users (IDUs), with contaminated needles, still hypoendemic in Sicily and the Mediterranean basin. Even though it is responsible for 20,000 to 40,000 deaths per year, this parasitic infection is still considered a neglected tropical disease. People Living with HIV (PLWH) are considered at high-risk of developing Leishmaniasis and, despite the introduction of Highly Active Anti-Retroviral Therapy (HAART), mortality rate and relapses prevalence are still high in coinfected people. CASE REPORT: We present a case of HIV-Leishmania coinfection, posing the attention on the atypical signs and symptoms and the importance of thinking about other causes than the HIV infection progression when the patient presents with a worsening of his immune status during HAART. CONCLUSION: This parasitic disease has a high mortality rate, so it is mandatory to think about it in all the patients having a low CD4+ T-cell count and an inverted CD4/CD8 ratio under HAART.
Simulation analysis of a Multiple Bus Shared Memory Multiprocessor

The past several years have brought the widespread acceptance of bus based shared memory parallel computer systems. There is a great deal of research which suggests that the limitations of single bus based interconnection networks prohibit effective use of more than perhaps 16 processors. Proposals have been made for several years [7] regarding the use of multiple buses to improve overall bandwidth. In research conducted during the past two years we have studied the performance gains which could be made by providing additional buses to interconnect processors and memory. In this paper we will present the results of extensive trace driven simulation done using a sample workload. Because a detailed simulation model was created we are able to obtain fine grain detail regarding the operation of the system.
An automatic acquisition of hierarchical mathematical morphology procedures by GA

This paper presents a method to obtain an image processing procedure by showing an original image and a target image. There are some preceding works concerns with automatic acquisition of image processing procedures by combining subroutine packages. In our approach, we only use the hierarchical mathematical morphology procedures, i.e., erosion and dilation operations. Since the subroutine packages are macro procedures, we use micro operations for constructing more flexible visual procedures. We use genetic algorithms (GA) to search procedures. Utilizing a parallel searching function of GA and introducing a concept of era, we construct hierarchical procedures of mathematical morphology.
Muscle Activation in Unilateral Barbell Exercises: Implications for Strength Training and Rehabilitation.

Mausehund, L, Skard, AE, and Krosshaug, T. Muscle activation in unilateral barbell exercises: Implications for strength training and rehabilitation. J Strength Cond Res XX(X): 000-000, 2018-The purpose of the present investigation was to assess lower-body muscle activity and hamstrings-to-quadriceps (HQ) activation ratios during performance of the split squat (SS), single-leg squat (SLS), and rear foot elevated split squat (RFESS), while using the same relative load and performing the exercises to muscular failure. Eleven healthy, moderately strength-trained subjects performed a 6-8 repetition maximum set of each exercise while electromyographic (EMG) activity of the vastus lateralis, biceps femoris, gluteus maximus, and gluteus medius was recorded. The results show that there were no significant differences in EMG peak activity of the gluteus maximus and vastus lateralis between any of the exercises. Gluteus medius activation was significantly (p ≤ 0.05) higher during the SLS (81.9% maximum voluntary isometric contraction [MVIC]), compared with the RFESS (54.9% MVIC) and SS (46.2% MVIC). The RFESS elicited higher (p ≤ 0.05) biceps femoris activity (76.1% MVIC) than the SS (62.3% MVIC), as well as higher (p ≤ 0.05) HQ activation ratios (0.83) than the SS (0.69) and SLS (0.63). During the SLS and the SS, HQ activation ratios increased significantly in the course of the repetition maximum set. In conclusion, although absolute loading differs between exercises, similar training stimuli of the gluteus maximus and quadriceps femoris can be expected for all exercises. The SLS is likely to induce the greatest improvements in gluteus medius strength, whereas the RFESS should be preferred if high hamstring coactivation is desired. To improve validity in EMG studies, strength training exercises should be performed close to failure while using the same relative loading.
2D Black Phosphorus: from Preparation to Applications for Electrochemical Energy Storage

Black phosphorus (BP) is rediscovered as a 2D layered material. Since its first isolation in 2014, 2D BP has triggered tremendous interest in the fields of condensed matter physics, chemistry, and materials science. Given its unique puckered monolayer geometry, 2D BP displays many unprecedented properties and is being explored for use in numerous applications. The flexibility, large surface area, and good electric conductivity of 2D BP make it a promising electrode material for electrochemical energy storage devices (EESDs). Here, the experimental and theoretical progress of 2D BP is presented on the basis of its preparation methods. The structural and physiochemical properties, air instability, passivation, and EESD applications of 2D BP are discussed systemically. Specifically, the latest research findings on utilizing 2D BP in EESDs, such as lithium‐ion batteries, supercapacitors, and emerging technologies (lithium–sulfur batteries, magnesium‐ion batteries, and sodium‐ion batteries), are summarized. On the basis of the current progress, a few personal perspectives on the existing challenges and future research directions in this developing field are provided.
Exploring the Effect of Monetary Incentives on User Behavior in Online Sharing Platforms

We examine the impact of monetary incentives on user onboarding in online sharing platforms. Specifically, drawing upon the literature of monetary incentives, privacy, and consumer behavior, we conduct a randomized field experiment to explore users’ initial engagement and interaction with an online car-sharing platform. Our empirical analyses show that monetary incentives are no better than simple email reminders in encouraging users’ self- disclosure of private information nor their active engagement with the platform (i.e., actual booking via the platform). Our work sheds new light on the heated debate over the design and deployment of monetary incentives in digital platforms, and provides useful implications for both academia and the industry.
Study of the relationship between peer-to-peer systems and IP multicasting

Peer-to-peer (P2P) systems, which have attracted public attention, involve a number of directly connected "peers" exchanging various types of information among themselves. However, applications based on P2P systems generally generate a lot of traffic and require not only the resources of every peer (e.g., CPU, memory, and bandwidth) but also many network resources. We think the main problems of P2P systems can be solved using IP multicasting, which is becoming popular as an effective way to transfer streaming media over the network and can reduce network traffic and the load on a streaming server. We propose applying IP multicasting to P2P systems. After mentioning that almost every application can be improved by our proposal, we discuss which routing protocol is suitable. Finally, we show that we can get good results even when part of the network does not support IP multicasting.
Developing a Mobile Application for Managing Anaphylaxis: Discovering Critical Success Factors

Anaphylaxis is a severe and potentially life-threatening allergic reaction that requires immediate treatment. A proposal for the development of a mobile application for supporting anaphylaxis patients was written by a team of allergists, after which this study was performed in order to identify critical success factors for the adoption of such an app. A mixed-method approach is used in order to gather data from a variety of sources, comprising a literature review, a domain expert interview, and a patient survey. One of the most valuable factors proved to be the validation of the medical information provided in the app. Besides this, patients are mostly concerned with the clarity of the presented information. While the proposed app does not fulfill all the identified factors, its development is overseen by medical professionals and endorsed by patient organizations. With a lack of such apps in the Dutch market and the demand indicated by survey respondents, this app has the potential to fill a gap in the support of anaphylaxis patients.
Microbiome in normal and pathological pregnancies: A literature overview

This review summarizes recent findings on the changes that occur during pregnancy in the composition of the vaginal and gut microbiome and their association with metabolic, hormonal, and immunological factors. Despite many studies on the topic, the vaginal and gut microbial profiles and their influence on the course of pregnancy are still unclear. We present data suggesting that, contrary to traditional understanding, the placenta is not sterile but has a microbial community. We review and discuss new findings on changes in the richness and diversity of the microbiota of pregnant women with term or preterm births, obesity, and gestational diabetes mellitus. Several factors influence the bacterial profile of these women and may explain, at least in part, some of the discrepant findings between studies. The development of and access to new molecular biology methods and techniques has expanded the possibilities of research. This will contribute to a better understanding of the microbiome and its role in normal and pathological pregnancies.
Role of capillary pericytes in the integration of spontaneous Ca2+ transients in the suburothelial microvasculature in situ of the mouse bladder

In the bladder suburothelial microvasculature, pericytes in different microvascular segments develop spontaneous Ca2+ transients with or without associated constrictions. Spontaneous Ca2+ transients in pericytes of all microvascular segments primarily rely on the cycles of Ca2+ uptake and release by the sarco‐ and endoplasmic reticulum. The synchrony of spontaneous Ca2+ transients in capillary pericytes exclusively relies on the spread of depolarizations resulting from the opening of Ca2+‐activated chloride channels (CaCCs) via gap junctions. CaCC‐dependent depolarizations further activate L‐type voltage‐dependent Ca2+ channels as required for the synchrony of Ca2+ transients in pericytes of pre‐capillary arterioles, post‐capillary venules and venules. Capillary pericytes may drive spontaneous Ca2+ transients in pericytes within the suburothelial microvascular network by sending CaCC‐dependent depolarizations via gap junctions.
Common signalling pathways in macrophage and osteoclast multinucleation

ABSTRACT Macrophage cell fusion and multinucleation are fundamental processes in the formation of multinucleated giant cells (MGCs) in chronic inflammatory disease and osteoclasts in the regulation of bone mass. However, this basic cell phenomenon is poorly understood despite its pathophysiological relevance. Granulomas containing multinucleated giant cells are seen in a wide variety of complex inflammatory disorders, as well as in infectious diseases. Dysregulation of osteoclastic bone resorption underlies the pathogenesis of osteoporosis and malignant osteolytic bone disease. Recent reports have shown that the formation of multinucleated giant cells and osteoclast fusion display a common molecular signature, suggesting shared genetic determinants. In this Review, we describe the background of cell–cell fusion and the similar origin of macrophages and osteoclasts. We specifically focus on the common pathways involved in osteoclast and MGC fusion. We also highlight potential approaches that could help to unravel the core mechanisms underlying bone and granulomatous disorders in humans. Summary: This Review highlights the common signalling pathways in macrophage and osteoclast multinucleation. This basic cell phenomenon which underlies various complex diseases is poorly understood.
Can we Learn from Down Under How to Rise Up in E-Government? A Comparative Analysis of the Public Sector Competences in the German and Australian Higher Education Systems

Australia has been voted world’s second in the last two United Nations e-government surveys 2014 and 2016, despite the acknowledged difficulties that arise in terms of implementation because of its federal structure. Germany, having a similar federal structure, in contrast, only ranks 15th. The study at hand aims at eliciting, if this development can be ascribed to the higher public administration and e-government education landscape. By means of a content analysis, we examined 126 higher education study programmes with a link to the public sector in Australia and compared them to a similar study in Germany from the year 2015. Results show that there are indeed differences with respect to the delivered contents and the respective competences in Australia that might contribute to the different e-government development in the two countries: Higher levels of socio-technical courses and a more contextualised programme delivery in general are two of the main findings.
Cytochrome P450 research and The Journal of Biological Chemistry

In honor of the 100th birthday of Dr. Herbert Tabor, JBC's Editor-in-Chief for 40 years, I will review here JBC's extensive coverage of the field of cytochrome P450 (P450) research. Research on the reactions catalyzed by these enzymes was published in JBC before it was even realized that they were P450s, i.e. they have a “pigment” with an absorption maximum at 450 nm. After the P450 pigment discovery, reported in JBC in 1962, the journal proceeded to publish the methods for measuring P450 activities and many seminal findings. Since then, the P450 field has grown extensively, with significant progress in characterizing these enzymes, including structural features, catalytic mechanisms, regulation, and many other aspects of P450 biochemistry. JBC has been the most influential journal in the P450 field. As with many other research areas, Dr. Tabor deserves a great deal of the credit for significantly advancing this burgeoning and important topic of research.