Miracle-dz/UniFAR-FTUs huggingface dataset:
With one it is easy, with many it gets complicated: Understanding Channel Security for Groups

Secure messaging systems such as TextSecure and Signal aim, among others, at providing authenticated and confidential channels between two or more communicating users. The general understanding seems to be that providing security in the sense of authenticated encryption (AE) for every point-to-point link suffices to make the constructed messaging systems secure, i.e., authentic and confidential. However, as recently shown (in FSE17/ToSC17), in the bidirectional (two-party) case, just requiring the two unidirectional links to provide security independently of each other does not lead to a secure communication channel in general. Briefly, the reason for this is that security notions need to take into account the increased level of interaction between users. This also applies, a fortiori, in a multi-user setting where many parties communicate concurrently and in multiple directions. We observe that in the current academic literature there is no rigorous definition of security for (broadcast) group communication. Applying the method of provable security, we fill this gap by defining security goals and showing how to provably achieve them. Concretely, the contributions of this paper are as follows: We develop a set of formal definitions of security goals for broadcast communication, capturing targets like confidentiality and authenticity. Our notions in particular take into account the causal dependencies that exchanged messages might have. (Note that these have no counterpart in the much simpler unidirectional case.) We then switch to the constructive side, designing an efficient protocol that requires only reliable point-to-point links between users and a standard cryptographic building block (AEAD), achieving all security goals defined in this paper. Our work thus paves the ground towards understanding the exact level of security that current secure messaging systems achieve.
Measuring the edge recombination velocity of monolayer semiconductors

Understanding edge effects and quantifying their impact on the carrier properties of two-dimensional (2D) semiconductors is an essential step toward utilizing these materials for high performance electronic and optoelectronic devices.1–5 WS2 monolayers patterned into disks of varying diameters are used to experimentally determine the influence of edges on their optical properties. Carrier lifetime measurements show a decrease in the effective lifetime, τeffective, as a function of decreasing diameter, suggesting that the edges are active sites for carrier recombination. Accordingly, we introduce a metric called edge recombination velocity (ERV) to characterize the impact of 2D material edges on non-radiative recombination. The unpassivated WS2 monolayer disks yield an ERV ∼ 4 × 104 cm/s. This work quantifies the non-radiative recombination edge effects in monolayer semiconductors, while simultaneously establishing a practical characterization technique towards experimental explorations of edge passivation methods for 2D materials.
Nitrification, denitrification, and dephosphatation capability of activated sludge during co-treatment of intermediate-age landfill leachates with municipal wastewater

ABSTRACT This study focuses on the possible use and efficacy of the co-treatment of landfill leachate (intermediate-age) with municipal wastewater. The nitrification, denitrification, and dephosphatation capability of activated sludge acclimated with a mixture of raw municipal wastewater (RWW) with gradually increasing amounts of raw landfill leachate (RLL) (from 0.5 to 5% v/v) were tested. Biochemical tests were conducted simultaneously in batch reactors (BRs). According to the obtained data, the ammonia utilization rate (AUR) was 3.68 g N/(kg volatile suspended solids (VSS)·h) for RWW, and it increased to 5.78 g N/(kg VSS·h) with the addition of 5% RLL. The nitrate utilization rate under anoxic conditions (NURAX) remained at a comparable level of 1.55–1.98 g N/(kg VSS·h). During the anoxic phase, both nitrate utilization and phosphorus uptake occurred, suggesting that denitrifying phosphorus-accumulating organisms (DPAOs) utilized N–NO3. With the addition of RLL, the rates of anoxic and aerobic phosphate uptake (PURAX and PURAE) and phosphate release rate (PRR) decreased. The PRR was likely negatively influenced by high N–NO3 concentrations but not completely inhibited due to the availability of a biodegradable fraction of chemical oxygen demand (COD). Thus, monitoring the NH4–N load in wastewater treatment plant influent before co-treatment is more informative than that using hydraulic-based criteria. Abbreviations: σ – standard deviation; AUR – ammonia utilization rate; DPAO – denitrifying phosphorus-accumulating organisms; MLVSS – mixed liquor volatile suspended solids content; MSW – municipal solid waste; NURAE – nitrate production rate under aerobic conditions; NURAX – nitrate utilization rate under anoxic conditions; PAO – phosphorus-accumulating organisms; PRR – phosphate release rate under anaerobic conditions; PURAX – phosphate uptake rate under anoxic conditions; PURAE – phosphate uptake rate under aerobic conditions; RLL – raw landfill leachates; RM0.5 – raw mixture of RWW with 0.5% (vol.) of RLL; RM3 – raw mixture of RWW with 3% (vol.) of RLL; RM5 – raw mixture of RWW with 5% (vol.) of RLL; RWW – wastewater; VFA – volatile fatty acids; WWTP – wastewater treatment plant
How oxygen gave rise to eukaryotic sex

How did full meiotic eukaryotic sex evolve and what was the immediate advantage allowing it to develop? We propose that the crucial determinant can be found in internal reactive oxygen species (ROS) formation at the start of eukaryotic evolution approximately 2 × 109 years ago. The large amount of ROS coming from a bacterial endosymbiont gave rise to DNA damage and vast increases in host genome mutation rates. Eukaryogenesis and chromosome evolution represent adaptations to oxidative stress. The host, an archaeon, most probably already had repair mechanisms based on DNA pairing and recombination, and possibly some kind of primitive cell fusion mechanism. The detrimental effects of internal ROS formation on host genome integrity set the stage allowing evolution of meiotic sex from these humble beginnings. Basic meiotic mechanisms thus probably evolved in response to endogenous ROS production by the ‘pre-mitochondrion’. This alternative to mitosis is crucial under novel, ROS-producing stress situations, like extensive motility or phagotrophy in heterotrophs and endosymbiontic photosynthesis in autotrophs. In multicellular eukaryotes with a germline–soma differentiation, meiotic sex with diploid–haploid cycles improved efficient purging of deleterious mutations. Constant pressure of endogenous ROS explains the ubiquitous maintenance of meiotic sex in practically all eukaryotic kingdoms. Here, we discuss the relevant observations underpinning this model.
Bioinspired Technologies to Connect Musculoskeletal Mechanobiology to the Person for Training and Rehabilitation

Musculoskeletal tissues respond to optimal mechanical signals (e.g., strains) through anabolic adaptations, while mechanical signals above and below optimal levels cause tissue catabolism. If an individual's physical behavior could be altered to generate optimal mechanical signaling to musculoskeletal tissues, then targeted strengthening and/or repair would be possible. We propose new bioinspired technologies to provide real-time biofeedback of relevant mechanical signals to guide training and rehabilitation. In this review we provide a description of how wearable devices may be used in conjunction with computational rigid-body and continuum models of musculoskeletal tissues to produce real-time estimates of localized tissue stresses and strains. It is proposed that these bioinspired technologies will facilitate a new approach to physical training that promotes tissue strengthening and/or repair through optimal tissue loading.
YopT domain of the PfhB2 toxin from Pasteurella multocida: protein expression, characterization, crystallization and crystallographic analysis.

Pasteurella multocida causes respiratory-tract infections in a broad range of animals, as well as opportunistic infections in humans. P. multocida secretes a multidomain toxin called PfhB2, which contains a YopT-like cysteine protease domain at its C-terminus. The YopT domain of PfhB2 contains a well conserved Cys-His-Asp catalytic triad that defines YopT family members, and shares high sequence similarity with the prototype YopT from Yersinia sp. To date, only one crystal structure of a YopT family member has been reported; however, additional structural information is needed to help characterize the varied substrate specificity and enzymatic action of this large protease family. Here, a catalytically inactive C3733S mutant of PfhB2 YopT that provides enhanced protein stability was used with the aim of gaining structural insight into the diversity within the YopT protein family. To this end, the C3733S mutant of PfhB2 YopT has been successfully cloned, overexpressed, purified and crystallized. Diffraction data sets were collected from native crystals to 3.5 Å resolution and a single-wavelength anomalous data set was collected from an iodide-derivative crystal to 3.2 Å resolution. Data pertaining to crystals belonging to space group P31, with unit-cell parameters a = 136.9, b = 136.9, c = 74.7 Å for the native crystals and a = 139.2, b = 139.2, c = 74.7 Å for the iodide-derivative crystals, are discussed.
EP300 contributes to high-altitude adaptation in Tibetans by regulating nitric oxide production

The genetic adaptation of Tibetans to high altitude hypoxia likely involves a group of genes in the hypoxic pathway, as suggested by earlier studies. To test the adaptive role of the previously reported candidate gene EP300 (histone acetyltransferase p300), we conducted resequencing of a 108.9 kb gene region of EP300 in 80 unrelated Tibetans. The allele-frequency and haplotype-based neutrality tests detected signals of positive Darwinian selection on EP300 in Tibetans, with a group of variants showing allelic divergence between Tibetans and lowland reference populations, including Han Chinese, Europeans, and Africans. Functional prediction suggested the involvement of multiple EP300 variants in gene expression regulation. More importantly, genetic association tests in 226 Tibetans indicated significant correlation of the adaptive EP300 variants with blood nitric oxide (NO) concentration. Collectively, we propose that EP300 harbors adaptive variants in Tibetans, which might contribute to high-altitude adaptation through regulating NO production.
Correlation of protein content of feedstuffs with the magnitude of nitrogen correction in true metabolizable energy determinations.

The relationship between the protein content of feedstuffs and the magnitude of difference between corresponding true metabolizable energy (TME) and nitrogen-corrected TME ( TMEn ) was investigated. Fifty-two samples of feed ingredients, mixtures of ingredients, and mixed feeds were assayed for TME and TMEn . A positive relationship was observed between the protein content of the feed samples and the magnitude of difference between determined TME and TMEn values. The regression equation describing this relationship is Y = . 122X + 3.724, where X equals percent protein and Y the percent difference between TME and TMEn . The corresponding r2 was . 60.
A Leakage-Abuse Attack Against Multi-User Searchable Encryption

Abstract Searchable Encryption (SE) allows a user to upload data to the cloud and to search it in a remote fashion while preserving the privacy of both the data and the queries. Recent research results describe attacks on SE schemes using the access pattern, denoting the ids of documents matching search queries, which most SE schemes reveal during query processing. However SE schemes usually leak more than just the access pattern, and this extra leakage can lead to attacks (much) more harmful than the ones using basic access pattern leakage only. We remark that in the special case of Multi-User Searchable Encryption (MUSE), where many users upload and search data in a cloud-based infrastructure, a large number of existing solutions have a common leakage in addition to the well-studied access pattern leakage. We show that this seemingly small extra leakage allows a very simple yet powerful attack, and that the privacy degree of the affected schemes have been overestimated. We also show that this new vulnerability affects existing software. Finally we formalize the newly identified leakage profile and show how it relates to previously defined ones.
Coverage probability of distributed wireless power transfer system

The wireless power transfer via an electro-magnetic (EM) wave enables far-field power transfer. In this paper, we provide an analytic and experimental study on a distributed antenna system for the wireless power transfer as a mean to overcome low end-to-end power transfer efficiency of a conventional collocated antenna system. We study the wireless power transfer system with or without the frequency and phase synchronization between antennas. Based on the experimental results, we show that the distributed antenna system is advantageous in terms of the coverage probability as long as the optimal distributed beamforming is available in the distributed antenna system.
Data-driven identification of potential Zika virus vectors

Zika is an emerging virus whose rapid spread is of great public health concern. Knowledge about transmission remains incomplete, especially concerning potential transmission in geographic areas in which it has not yet been introduced. To identify unknown vectors of Zika, we developed a data-driven model linking vector species and the Zika virus via vector-virus trait combinations that confer a propensity toward associations in an ecological network connecting flaviviruses and their mosquito vectors. Our model predicts that thirty-five species may be able to transmit the virus, seven of which are found in the continental United States, including Culex quinquefasciatus and Cx. pipiens. We suggest that empirical studies prioritize these species to confirm predictions of vector competence, enabling the correct identification of populations at risk for transmission within the United States.
Real Time Collision Detection and Identification for Robotic Manipulators

The majority of everyday tasks involve interacting with unstructured environments. This implies that, in order for robots to be truly useful they must be able to handle contacts. This paper explores how a particle filter can be used to localize a contact point and estimate the external force. We demonstrate the capability of the particle filter on a simulated 4DoF planar robotic arm, and compare it to a well-established analytical approach.
Comparison of dwarf and normal broiler breeder hens.

Two strains of dwarf and two of normal broiler breeder hens were compared during the laying period for the following production parameters: egg number, hen-day and hen-housed egg production, mortality, feed consumption, egg weight, egg shell quality, hatchability, and fertility. Though the dwarf hens matured earlier, the number of eggs produced during the laying period did not differ (P less than .05) from that of the normal hens. The dwarf hens consumed 25.6% less feed per dozen eggs but produced smaller eggs. Mortality was higher for the dwarf hens during the laying period than for normal hens. The normal hens had an advantage over the dwarf hens in percent hatchability of all eggs set and percent fertility, but the percent hatchability of fertile eggs did not differ between the two genetic groups. No differences were found in egg shell quality of the two groups of chickens.
Thyroid function, growth hormone, and organ growth in broilers deficient in phosphorus.

The effects of a dietary P deficiency on thyroid function, serum growth hormone, and growth parameters in 10 to 29-day-old broiler cockerels was determined. Chicks fed severely P-deficient diets (.05% or .10% available P) grew more slowly and ate less feed than controls fed . 65% P. The deficiency was also accompanied by hypercalcemia, hypophosphatemia, and decreases in percent bone ash, fat-free tibial weight, and tibial length and width. Increases in the relative weights of kidneys, hearts, and pituitary glands (.05% P only) occurred as well. Most of these changes occurred to a lesser extent or not at all in pair-fed controls, showing that they resulted specifically from the P deficiency and were not simply a result of reductions in feed intake. Phosphorus deficiency also was accompanied by peripheral edema and hydropericardium. Relative thyroid weight was unaffected. Serum triiodothyronine was consistently lower in the P-deficient chicks, although effects were significant only in one experiment. Thyroxine levels tended to be low also, but not consistently so. Serum growth hormone in P-deficient chicks in both studies was consistently lower than that in pair-fed controls, but this was significant only when . 10% but not . 05% available P was fed. The findings suggest that serum levels of both thyroid hormone and growth hormone are altered by P deficiency, but the results were not clearly definitive.
History rather than hybridization determines population structure and adaptation in Populus balsamifera

Hybridization between species is known to greatly affect their genetic diversity and, therefore, their evolution. Also, within species, there may be genetic clusters between which gene flow is limited, which may impact natural selection. However, few studies have looked simultaneously at the influence of among‐species and within‐species gene flow. Here, we study the influence of hybridization between Populus balsamifera and Populus trichocarpa on population structure and adaptation in P. balsamifera. We did this by sampling a total of 1517 individuals from across the ranges of these two species, and by genotyping them using a combination of 93 nuclear and 17 cpDNA SNPs. We found that hybridization is mostly limited to the contact zone where the species’ distributions overlap. Within P. balsamifera, we found multiple levels of population structure. Interestingly, the border between the Eastern and Central clusters is very sharp, whereas the border between the Central and Western clusters is diffuse. Outlier analysis revealed that three loci associated with the sharp border were also associated with climate. We hypothesize that the observed clusters derive from three refugia during the Pleistocene ice ages. Between the Central and Western clusters, post‐glacial long‐distance gene flow has led to the diffusion of their border. In the Eastern cluster, we hypothesize that endogenous genomic barriers have developed, leading to the sharp border and a spurious climate association. We conclude that the large‐scale genetic structure of P. balsamifera is mostly shaped by historical factors and the influence of interspecific hybridization is limited.
Expression Patterns and Identified Protein-Protein Interactions Suggest That Cassava CBL-CIPK Signal Networks Function in Responses to Abiotic Stresses

Cassava is an energy crop that is tolerant of multiple abiotic stresses. It has been reported that the interaction between Calcineurin B-like (CBL) protein and CBL-interacting protein kinase (CIPK) is implicated in plant development and responses to various stresses. However, little is known about their functions in cassava. Herein, 8 CBL (MeCBL) and 26 CIPK (MeCIPK) genes were isolated from cassava by genome searching and cloning of cDNA sequences of Arabidopsis CBLs and CIPKs. Reverse-transcriptase polymerase chain reaction (RT-PCR) analysis showed that the expression levels of MeCBL and MeCIPK genes were different in different tissues throughout the life cycle. The expression patterns of 7 CBL and 26 CIPK genes in response to NaCl, PEG, heat and cold stresses were analyzed by quantitative real-time PCR (qRT-PCR), and it was found that the expression of each was induced by multiple stimuli. Furthermore, we found that many pairs of CBLs and CIPKs could interact with each other via investigating the interactions between 8 CBL and 25 CIPK proteins using a yeast two-hybrid system. Yeast cells co-transformed with cassava MeCIPK24, MeCBL10, and Na+/H+ antiporter MeSOS1 genes exhibited higher salt tolerance compared to those with one or two genes. These results suggest that the cassava CBL-CIPK signal network might play key roles in response to abiotic stresses.
Automatic registration of large set of microscopic images using high-level features

In this paper, we present a novel method for automatic registration of large set of microscopic images by automatically match high-level region features via finding cyclic structures in a matching graph. The use of high-level features (e.g., regions, landmarks, objects) significantly reduced the computation and provides accurate initialization, which further allows fast convergence of the maximum mutual information algorithm. The scheme is a universal one as it works for other types of high-level features and the matching process is very computationally efficient. We have applied our method in 3-D reconstruction of a unique human cochlear sample and are also applying it to two other set of large microscopic images
High intake of heterocyclic amines from meat is associated with oxidative stress

High meat intake has been related to chronic diseases such as cancer and CVD. One hypothesis is that heterocyclic amines (HCA), which are formed during the cooking process of meat, can generate reactive species. These compounds can cause oxidation of lipids, proteins and DNA, resulting in oxidative stress, cell damage and loss of biological function. This association has been seen in vitro; however, it remains unclear in vivo. The aim of the present study was to investigate the association between oxidative stress and HCA intake, and oxidative stress and meat intake. Data were from the Health Survey for Sao Paulo – ISA-Capital (561 adult and elderly). Food intake was estimated by one 24-h dietary recall (24HR) complemented by a detailed FFQ with preferences of cooking methods and level of doneness for meat. HCA intake was estimated linking the meat from the 24HR to a database of HCA. Oxidative stress was estimated by malondialdehyde (MDA) concentration in the plasma, after derivatisation with thiobarbituric acid and quantification by HPLC/diode array. Analyses were performed using multivariate logistic regressions adjusted for smoking, sex, age, BMI, skin colour, energy intake, fruit and vegetable intake, and physical activity. A positive association between HCA intake and MDA concentration (OR 1·17; 95 % CI 1·01, 1·38) was observed, showing that HCA from meat may contribute to increase oxidative stress, and may consequently increase the risk of chronic diseases.