Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconsidering an active role for G-actin in cytoskeletal regulation

ABSTRACT Globular (G)-actin, the actin monomer, assembles into polarized filaments that form networks that can provide structural support, generate force and organize the cell. Many of these structures are highly dynamic and to maintain them, the cell relies on a large reserve of monomers. Classically, the G-actin pool has been thought of as homogenous. However, recent work has shown that actin monomers can exist in distinct groups that can be targeted to specific networks, where they drive and modify filament assembly in ways that can have profound effects on cellular behavior. This Review focuses on the potential factors that could create functionally distinct pools of actin monomers in the cell, including differences between the actin isoforms and the regulation of G-actin by monomer binding proteins, such as profilin and thymosin β4. Owing to difficulties in studying and visualizing G-actin, our knowledge over the precise role that specific actin monomer pools play in regulating cellular actin dynamics remains incomplete. Here, we discuss some of these unanswered questions and also provide a summary of the methodologies currently available for the imaging of G-actin. Summary: This Review provides an overview of how the cell regulates its actin monomer pool, focusing on factors that could create distinct groups of G-actin, and proposes an active role for G-actin in cytoskeletal dynamics.
Reevaluation of nonphytate phosphorus requirement of growing pullets with and without phytase.

An experiment was conducted to re-evaluate the nonphytate phosphorus (NPP) requirement of growing pullets and to determine to what extent this requirement could be reduced by phytase. Six diets in a 3 x 2 factorial design were used. The pullets of the control group (T1) were fed a sequence of 0.4-0.35-0.3% NPP for the age periods of 0 to 6, 6 to 12, and 12 to 18 wk, respectively, according to NRC (1994) recommendation. The NPP level was reduced by an increment of 0.1% in each phase in T2 and T3. The pullets of T4 to T6 were fed similar NPP levels to T1 to T3, respectively, with 300 units phytase/kg diet. From 18 to 30 wk of age, the pullets on all growing regimens were fed a layer diet with 0.4% NPP. Records were maintained for BW and feed intake during the growing period and for egg production during the laying period. Blood and tibia samples were taken at 6, 12, and 18 wk of age for determining plasma P, tibia weight, and tibia ash. Two digestion trials were conducted at Weeks 5 and 18 for determining total P excretion. Body weights at 18 wk and feed intake for the period of 0 to 18 wk were not different from the control for pullets fed the two lower NPP regimens (P > 0.05). Phytase had a favorable effect on BW at 18 wk (P = 0.0539) and feed intake for the period of 0 to 18 wk (P < 0.05). Plasma P was lower for pullets fed the least NPP than for those fed the control NPP regimen only at 6 wk of age (P < 0.05). Bone quality measurements at 6, 12, and 18 wk of age were not different for pullets fed various NPP regimens (P > 0.05). Phytase, for the most part did, not have an effect on plasma P and bone quality (P > 0.05). Total P intake and total P excretion (mg/bird per day) were reduced due to lowering the dietary NPP in both digestion trials (P < 0.05). Phytase did not have an effect on daily total P intake or excretion. Production and specific gravity were not influenced by NPP regimens used during the growing period. Specific gravity for the entire experiment was greater for pullets fed phytase (P < 0.05). The results indicated that the lowest NPP regimen in the absence of phytase was adequate to support performance of pullets, and due to this, it was not possible to determine the effect of phytase in diminishing the P need of growing pullets.
Feature Extraction based on Touch Interaction Data in Virtual Reality-based IADL for Characterization of Mild Cognitive Impairment

The aim of this study was to explore the feature pattern of Mild Cognitive Impairment (MCI) in Virtual Reality based Instrumental Activities of Daily Living (VR-IADL) which runs on a tablet PC as well as requires participants a touch interaction to complete the task. Twelve participants (MCI: 4, history of MCI: 2, healthy elderly: 6) were recruited from the region of Philadelphia in USA to perform a VR-IADL task. We found that Non Touch Time (NTT) which is time interval during not touching screen on tablet was longer than that of MCI patients as well as healthy older adults with having history of MCI. Several types of feature patterns were extracted from the NTT such as . Based on the feature pattern, Support Vector Machine (SVM) was performed to calculate the accuracy of the feature patter for characterization of MCI. As the result, the identification rate was 75%.
Estimates of quantitative genetic parameters of immunological traits in the chicken.

Three in vivo assays were used to measure the immunocompetence of chickens in two generations of a selection experiment. The obtained data were used to estimate the variance components for sire and dam for antibody production to Pasteurella multocida and Mycoplasma gallisepticum vaccines, for T-cell-mediated immunity evaluated by a phytohemagglutinin wing web assay, and for clearance of foreign particles from the circulatory system. Heritabilities of and genetic correlations among these immunological traits were calculated from the sire variance components. Heritability estimates of the immunological traits based on the sire component of variance ranged from . 06 to . 53, and genetic correlations among immunological traits were generally negative.
A trypsin-like enzyme in acrosomal extracts of chicken, turkey and quail spermatozoa.

Abstract The presence of an active trypsin-like enzyme in the acrosomes of chicken, turkey and quail spermatozoa was evaluated. Pooled semen samples (0.5 ml.) were collected from each species and the sperm washed several times with modified Ringer’s solution. Acrosomal extracts were prepared and assayed for trypsin-like enzyme by the presence of esterase activity using TAME (p-toluensulfonyl- l -arginine methyl ester) as a substrate and measuring the change in optical density per minute at 247 mμ. Esterase activity of acrosomal extracts obtained from recently ejaculated spermatozoa of the chicken, turkey and quail indicate that an active trypsin-like enzyme is present in the acrosomes of spermatozoa from all three of these species.
Proteomic insights into extracellular vesicle biology – defining exosomes and shed microvesicles

ABSTRACT Introduction: Extracellular vesicles (EVs) are critical mediators of intercellular communication, capable of regulating the transcriptional landscape of target cells through horizontal transmission of biological information, such as proteins, lipids, and RNA species. This capability highlights their potential as novel targets for disease intervention. Areas covered: This review focuses on the emerging importance of discovery proteomics (high-throughput, unbiased quantitative protein identification) and targeted proteomics (hypothesis-driven quantitative protein subset analysis) mass spectrometry (MS)-based strategies in EV biology, especially exosomes and shed microvesicles. Expert commentary: Recent advances in MS hardware, workflows, and informatics provide comprehensive, quantitative protein profiling of EVs and EV-treated target cells. This information is seminal to understanding the role of EV subtypes in cellular crosstalk, especially when integrated with other ‘omics disciplines, such as RNA analysis (e.g., mRNA, ncRNA). Moreover, high-throughput MS-based proteomics promises to provide new avenues in identifying novel markers for detection, monitoring, and therapeutic intervention of disease.
Analysis of Sparse Cutting Planes for Sparse MILPs with Applications to Stochastic MILPs

In this paper, we present an analysis of the strength of sparse cutting-planes for mixed integer linear programs (MILP) with sparse formulations. We examine three kinds of problems: packing problems, covering problems, and more general MILPs with the only assumption that the objective function is non-negative. Given a MILP instance of one of these three types, assume that we decide on the support of cutting-planes to be used and the strongest inequalities on these supports are added to the linear programming relaxation. Call the optimal objective function value of the linear programming relaxation together with these cuts as $z^{cut}$. We present bounds on the ratio of $z^{cut}$ and the optimal objective function value of the MILP that depends only on the sparsity structure of the constraint matrix and the support of sparse cuts selected, that is, these bounds are completely data independent. These results also shed light on the strength of scenario-specific cuts for two stage stochastic MILPs.
Adaptive input data transformation for improved network reconstruction with information theoretic algorithms

Abstract We propose a novel systematic procedure of non-linear data transformation for an adaptive algorithm in the context of network reverse-engineering using information theoretic methods. Our methodology is rooted in elucidating and correcting for the specific biases in the estimation techniques for mutual information (MI) given a finite sample of data. These are, in turn, tied to lack of well-defined bounds for numerical estimation of MI for continuous probability distributions from finite data. The nature and properties of the inevitable bias is described, complemented by several examples illustrating their form and variation. We propose an adaptive partitioning scheme for MI estimation that effectively transforms the sample data using parameters determined from its local and global distribution guaranteeing a more robust and reliable reconstruction algorithm. Together with a normalized measure (Shared Information Metric) we report considerably enhanced performance both for in silico and real-world biological networks. We also find that the recovery of true interactions is in particular better for intermediate range of false positive rates, suggesting that our algorithm is less vulnerable to spurious signals of association.
To catch a fake: Curbing deceptive Yelp ratings and venues

The popularity and influence of reviews, make sites like Yelp ideal targets for malicious behaviors. We present Marco, a novel system that exploits the unique combination of social, spatial and temporal signals gleaned from Yelp, to detect venues whose ratings are impacted by fraudulent reviews. Marco increases the cost and complexity of attacks, by imposing a tradeoff on fraudsters, between their ability to impact venue ratings and their ability to remain undetected. We contribute a new dataset to the community, which consists of both ground truth and gold standard data. We show that Marco significantly outperforms state‐of‐the‐art approaches, by achieving 94% accuracy in classifying reviews as fraudulent or genuine, and 95.8% accuracy in classifying venues as deceptive or legitimate. Marco successfully flagged 244 deceptive venues from our large dataset with 7,435 venues, 270,121 reviews and 195,417 users. Furthermore, we use Marco to evaluate the impact of Yelp events, organized for elite reviewers, on the hosting venues. We collect data from 149 Yelp elite events throughout the US. We show that two weeks after an event, twice as many hosting venues experience a significant rating boost rather than a negative impact.
2015 Ieee International Conference on Big Data (big Data) Bandwidth-efficient Distributed K-nearest-neighbor Search with Dynamic Time Warping

—We study the fundamental k-nearest neighbor (kNN) search problem on distributed time series. A server has constantly received various reference time series Q of length X and seeks the exact kNN over a collection of time series distributed across a set of M local sites. When X and M are large, and when the amount of query increases, simply sending each Q to all M sites incurs high communication bandwidth costs, which we would like to avoid. Prior work has presented a communication-efficient kNN algorithm for the Euclidean distance similarity measure. In this paper, we present the first communication-efficient kNN algorithm for the dynamic time warping (DTW) similarity measure, which is generally believed a better measure for time series. To handle the complexities of DTW, we design a new multi-resolution structure for the reference time series, and multi-resolution lower bounds that can effectively prune the search space. We present a new protocol between the server and the local sites that leverages multi-resolution pruning for communication efficiency and cascading lower bounds for computational efficiency. Empirical studies on both real-world and synthetic data sets show that our method reduces communication bandwidth by up to 92%.
The effect of genetic origin, source of antigen, and dose of antigen on the immune response of cockerels.

The total agglutinin antibody titers and the 2-mercaptoethanol resistant antibody titers were determined in cockerels of three genetic origins, i.e., White Plymouth Rock (WPR), White Leghorn (WL), and a medium heavy breed cross (Warren). At 34 days of age the chicks were injected i.m. with 1.0 ml of either 100, 10, or 1% suspension of packed sheep red blood cells (SRBC) in phosphate buffered saline. Antibody titers were determined on days 0, 3, 7, and 14 postinjection. The response to phytohemagglutinin (PHA) was measured at 49 days of age after intradermal injections of the antigen into the wingweb of the birds that had received the 100% suspension of SRBC. Differences among genetic groups resulted in significant differences for total antibody titers. The ranking of groups of different origin varied with day postinjection. The highest antigen dose yielded the highest antibody titers and there were no significant genetic origin-dose interactions. The WPR cockerels showed the greatest swelling in the PHA test, followed by the Warren and WL in that order, with differences being significant (P less than .05). There was no correlation between antibody titers to SRBC measured on day 3, 7, and 14 postinjection and PHA response, either overall or within groups of different genetic origin. We tentatively conclude that selection for general immune responsiveness may mean combining parameters of antibody and cell-mediated immune responses. The WPR cockerels were significantly (P less than .005) heavier than the Warren cockerels, which in turn were significantly heavier (P less than .005) than the WL. Statistical analyses suggest that the antibody response may be independent of body weight differences within genetically similar groups.
Measurement of malabsorption of carotenoids in chickens with pale-bird syndrome.

Because pale-bird syndrome (PBS), defined as the failure of birds to realize the color potential of their diet, has been demonstrated to be caused by malabsorption or by hyperexcretion of carotenoids, a method for measuring malabsorption of carotenoids would be useful. The absorption of dietary canthaxanthin, a red diketocarotenoid, into serum during aflatoxicosis was measured in an experiment with a 2 x 9 factorial arrangement of treatments (0 and 5 micrograms of aflatoxin/g of diet; serum collected at 0, 2, 4, 6, 8, 10, 12, 14, and 24 h after a standard meal fed to four groups of 10 3-wk-old birds). Serum canthaxanthin levels determined by HPLC attained plateau values between 8 and 14 h after the meal. The absorption of canthaxanthin was depressed significantly (P less than .05) in birds with aflatoxicosis from 4 to 24 h after feeding the standard meal. Four field flocks diagnosed as having PBS were tested for malabsorption by intubating 10 birds with a standard amount of canthaxanthin and measuring serum canthaxanthin 12 h later. One flock had about 85% normally pigmented birds and 15% extremely pale birds, the second flock had a coccidiosis history, the third had a Newcastle disease history, and the fourth had a history of both coccidiosis and Newcastle disease. The flocks were 5- to 6-wk-old, received feed of the same manufacture, and their disease outbreaks had occurred 2 wk earlier. (ABSTRACT TRUNCATED AT 250 WORDS)
Breakdown Resilience of Key Exchange Protocols and the Cases of NewHope and TLS 1.3

Broken cryptographic algorithms and hardness assumptions are a constant threat to real-world protocols. Prominent examples are hash functions for which collisions become known, or number-theoretic assumptions which are threatened by advances in quantum computing. Especially when it comes to key exchange protocols, the switch to quantum-resistant primitives has begun and aims to protect today’s secrets against future developments, moving from common Diffie–Hellmanbased solutions to Learning-With-Errors-based approaches. Remarkably, the authentication step in such protocols is usually still carried out with quantum-vulnerable signature schemes. The intuition here is that the adversary would need to break this protocol primitive today, without having quantum power yet. The question we address here is if this intuition is justified, and if so, if we can show this rigorously. To this date there exists no security notion for key exchange protocols that could capture the scenario of breakdowns of arbitrary cryptographic primitives to argue security of prior sessions. In this work we introduce an extension to the common Bellare–Rogaway model that can provide security guarantees in what we call the breakdown scenario and we term the resulting security notion breakdown resilience. The model allows to make security claims even in case of unexpected failure of primitives in the protocol, may it be hash functions, signature schemes, key derivation functions, etc. To validate the proposed security model with respect to real-world protocols we show that breakdown resilience for certain primitives is achieved by both an authenticated variant of the recently introduced post-quantum secure key exchange protocol NewHope (Alkim et al., USENIX Security 2016), as well as by TLS 1.3, which is currently being developed by the Internet Engineering Task Force.
A New Glaucoma Severity Score Combining Structural and Functional Defects

Abstract Background In order to assess glaucoma severity and to compare the success of surgical and medical therapy and study outcomes, an objective and independent staging tool is necessary. A combination of information from both structural and functional testing is probably the best approach to stage glaucomatous damage. There has been no universally accepted standard for glaucoma staging. The aim of this study was to develop a Glaucoma Severity Score (GSS) for objective assessment of a patientʼs glaucoma severity, combining both functional and structural information. Materials and methods The Glaucoma Severity Score includes the following 3 criteria: superior and inferior Retinal Nerve Fibre Layer (RNFL) thickness, perimetric mean defect (MD), and agreement of anatomical and perimetric defects, as assessed by two glaucoma specialists. The specialists defined a staging tool for each of the 3 criteria in a consensus process, assigning specific characteristics to a scale value between 0 and 2 or 0 and 3, respectively. The GSS ranges between 0 and 10 points. In a prospective observational study, the data of 112 glaucoma patients were assessed independently by the two specialists according to this staging tool. Results The GSS was applied to 112 eyes and patients (59.8 % female) with a mean age of 66.3 ± 13.1 years. Mean GSS was 4.73 points. Cohenʼs kappa coefficient was determined to measure inter-rater agreement between glaucoma specialists for the third criterion. With κ = 0.83, the agreement was very good. Thus, all 3 criteria of the GSS may be regarded as objective. Conclusions The Glaucoma Severity Score is an objective tool, combining both structural and functional characteristics, and permitting comparison of different patients, populations and studies. The Glaucoma Severity Score has proven effective in the objective assessment of 112 glaucoma patients and is relatively user-friendly in clinical practice. A comparative study of the GSS with the results of the FORUM® Glaucoma Workplace (Carl Zeiss Meditec AG, Jena, Germany) will be the next step. If outcomes match, the Glaucoma Severity Score can be accepted as a promising tool to stage glaucoma and monitor changes objectively in patients when comparing glaucoma progression in study analyses.
Diffuse Cystic Lung Diseases: Diagnostic Considerations

Abstract Diffuse cystic lung disease (DCLD) is a group of heterogeneous diseases that present as diffuse cystic changes in the lung on computed tomography of the chest. Most DCLD diseases are rare, although they might resemble common diseases such as emphysema and bronchiectasis. Main causes of DCLD include lymphangioleiomyomatosis, Birt–Hogg–Dubé syndrome, pulmonary Langerhans cell histiocytosis, lymphoid interstitial pneumonia, amyloidosis, light-chain deposition disease, Sjögren syndrome, and primary or metastatic neoplasm. We discuss clinical factors that are helpful in the differential diagnosis of DCLDsuch as sex and age, symptoms and signs, extrapulmonary presentations, cigarette smoking, and family history. Investigations for DCLD include high-resolution computed tomography, biochemical and histopathological studies, genetic tests, pulmonary function tests, and bronchoscopic and video-assisted thoracoscopic biopsies. A proposed diagnostic algorithm would enhance ease of diagnosing most cases of DCLD.
Comparison of the polymerase chain reaction using genus-specific oligonucleotide primers and microbiologic culture for the detection of Salmonella in drag-swabs from poultry houses.

Drag-swab samples were collected from 18 poultry houses at 9 broiler farms. Fifty drag-swab samples were tested for Salmonella by microbiologic culture using selective enrichment and the polymerase chain reaction (PCR) with oligonucleotide primers specific for all members of the genus Salmonella. Drag-swab samples were tested for Salmonella using PCR before and after enrichment. Only one sample was positive by PCR prior to enrichment. Forty-seven of the drag-swabs samples tested after enrichment were positive for Salmonella using PCR, and 29 were positive by microbiologic culture. All but one of the culture-positive samples were positive by PCR; this discordant sample was classified as indeterminate by PCR. Salmonella was identified in houses from all nine farms by PCR and eight of nine farms by microbiologic culture. Salmonella was found in all 18 houses by PCR and in 15 of 18 houses by microbiologic culture. In this study, PCR was significantly (P < .001) more sensitive than culture for environmental monitoring of Salmonella using drag-swabs.