Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular genetic studies on morphologically indistinguishable Myxobolus spp. infecting cyprinid fishes, with the description of three new species, M. alvarezae sp. nov., M. sitjae sp. nov. and M. eirasianus sp. nov.

While studying Myxobolus gill infections of cyprinid fishes, the authors found large, segmented plasmodia in three species: ide (Leuciscus idus), asp (Aspius aspius) and white bream (Blicca bjoerkna). As regards their size and morphology, the spores from these plasmodia corresponded to those of M. dujardini described from chub (Leuciscus cephalus). However, the 18S rDNA sequences of spores from the three cyprinids differed from those of M. dujardini. Based on molecular differences, this paper describes two new species: M. alvarezae sp. nov. from ide and asp, and M. sitjae sp. nov. from white bream. The two new species and M. dujardini had a similar tissue tropism, and infected the multilayered epithelium of the gill filaments. Histological examination of the infected filaments demonstrated that the large plasmodia with multiple buddings were formed from amalgamating small plasmodia. Besides carrying infection in the filamental epithelium, the three above fish species were infected by small intralamellar plasmodia as well. These plasmodia were filled by spores that resembled the roach parasite M. intimus both in morphology and seasonal development. The 18S rDNA sequences of ‘intimus-like’ spores from ide and asp differed only in some base pairs from spores found in the type host roach, and were identified as belonging to M. intimus. The spores found in white bream, however, showed 3.6-5.0% difference in DNA sequence from those of M. intimus; therefore, they have been described as M. eirasianus sp. nov. The aim of this paper was to demonstrate the importance of using molecular methods for separating and identifying morphologically corresponding or closely similar Myxobolus spp.
A study of reservation dynamics in integrated services packet networks

The integrated services packet network (ISPN) architecture proposed within the Internet community incorporates a resource reservation mechanism for those applications requiring quality of service (QoS) guarantees. Resource reservation introduces a new form of resource contention that can lead to reduced network throughput and thrashing. We establish several necessary conditions to induce thrashing. We also look at the effects several different reservation models and user behavior can have on network stability. Our work is unique from previous network resource reservation investigations in that we consider the effects of reservations for multipoint-to-multipoint applications. We conclude with examples of how simple modifications to user behavior can result in significant increases in system stability.
The outer membrane protease PgtE of Salmonella enterica interferes with the alternative complement pathway by cleaving factors B and H

The virulence factor PgtE is an outer membrane protease (omptin) of the zoonotic pathogen Salmonella enterica that causes diseases ranging from gastroenteritis to severe enteric fever. It is surface exposed in bacteria that have a short-chain, i.e., rough LPS, as observed e.g., in bacteria residing inside macrophages or just emerging from them. We investigated whether PgtE cleaves the complement factors B (B) and H (H), key proteins controlling formation and inactivation of the complement protein C3b and thereby the activity of the complement system. S. enterica serovar Typhimurium or omptin-expressing recombinant E. coli bacteria were incubated with purified human complement proteins or recombinant H fragments. PgtE cleaved both B and H, whereas its close homolog Pla of Yersinia pestis cleaved only H. H was cleaved at both N- and C-termini, while the central region resisted proteolysis. Because of multiple effects of PgtE on complement components (cleavage of C3, C3b, B, and H) we assessed its effect on the opsonophagocytosis of Salmonella. In human serum, C3 cleavage was dependent on proteolytically active PgtE. Human neutrophils interacted less with serum-opsonized FITC-stained S. enterica 14028R than with the isogenic ΔpgtE strain, as analyzed by flow cytometry. In conclusion, cleavage of B and H by PgtE, together with C3 cleavage, affects the C3-mediated recognition of S. enterica by human neutrophils, thus thwarting the immune protection against Salmonella.
The role of surgical debridement in healing of diabetic foot ulcers

An estimated 15% of patients with diabetes mellitus will develop a foot ulcer during their lifetime. Debridement is included in multiple guidelines and algorithms for the care of patients with diabetic neuropathic foot ulcers, and it has long been considered an essential step in the protocol for treating diabetic foot ulcers. In addition to altering the environment of the chronic wound, debridement is a technique aimed at removing nonviable and necrotic tissue, thought to be detrimental to healing. This is accomplished by removing abnormal wound bed and wound edge tissue, such as hyperkeratotic epidermis (callus) and necrotic dermal tissue, foreign debris, and bacteria elements known to have an inhibitory effect on wound healing. While the rationale for surgical debridement seems logical, the evidence for its role in enhancing healing is deficient. In this paper, we systematically review five published clinical trials, which met the criteria and investigated surgical debridement of diabetic foot ulcers to enhance healing. Most existing studies are not randomized clinical trials optimized to test the relationship between debridement of diabetic foot ulcers and wound healing. Therefore, a focused, well‐designed study is needed to elucidate the effect of surgical debridement on the healing status of chronic wounds.
The use of fractal analysis and photometry to estimate the accuracy of bulbar redness grading scales.

PURPOSE To use physical attributes of redness to determine the accuracy of four bulbar redness grading scales, and to cross-calibrate the scales based on these physical measures. METHODS Two image-processing metrics, fractal dimension (D) and percentage of pixel coverage (% PC), as well as photometric chromaticity were selected as physical measures, to describe and compare grades of bulbar redness among the McMonnies/Chapman-Davies scale, the Efron Scale, the Institute for Eye Research scale, and a validated scale developed at the Centre for Contact Lens Research. Two sets of images were prepared by using image processing: The first included multiple segments covering the largest possible region of interest (ROI) within the bulbar conjunctiva in the original images; the second contained modified scale images that were matched in size and resolution across scales, and a single, equally-sized ROI. To measure photometric chromaticity, the original scale images were displayed on a computer monitor, and multiple conjunctival segments were analyzed. Pearson correlation coefficients between each set of image metrics and the reference image grades were calculated to determine the accuracy of the scales. RESULTS Correlations were high between reference image grades and all sets of objective metrics (all Pearson's r >or= 0.88, P <or= 0.05); each physical attribute pointed to a different scale as being most accurate. Independent of the physical attribute used, there were wide discrepancies between scale grades, with almost no overlap when cross-calibrating and comparing the scales. CONCLUSIONS Despite the generally strong linear associations between the physical characteristics of reference images in each scale, the scales themselves are not inherently accurate and are too different to allow for cross-calibration.
Cascade convolutional neural networks for automatic detection of thyroid nodules in ultrasound images

Purpose It is very important for calculation of clinical indices and diagnosis to detect thyroid nodules from ultrasound images. However, this task is a challenge mainly due to heterogeneous thyroid nodules with distinct components are similar to background in ultrasound images. In this study, we employ cascade deep convolutional neural networks (CNNs) to develop and evaluate a fully automatic detection of thyroid nodules from 2D ultrasound images. Methods Our cascade CNNs are a type of hybrid model, consisting of two different CNNs and a new splitting method. Specifically, it employs a deep CNN to learn the segmentation probability maps from the ground true data. Then, all the segmentation probability maps are split into different connected regions by the splitting method. Finally, another deep CNN is used to automatically detect the thyroid nodules from ultrasound thyroid images. Results Experiment results illustrate the cascade CNNs are very effective in detection of thyroid nodules. Specially, the value of area under the curve of receiver operating characteristic is 98.51%. The Free‐response receiver operating characteristic (FROC) and jackknife alternative FROC (JAFROC) analyses show a significant improvement in the performance of our cascade CNNs compared to that of other methods. The multi‐view strategy can improve the performance of cascade CNNs. Moreover, our special splitting method can effectively separate different connected regions so that the second CNN can correctively gain the positive and negative samples according to the automatic labels. Conclusions The experiment results demonstrate the potential clinical applications of this proposed method. This technique can offer physicians an objective second opinion, and reduce their heavy workload so as to avoid misdiagnosis causes because of excessive fatigue. In addition, it is easy and reproducible for a person without medical expertise to diagnose thyroid nodules.
Distorted Fingerprint Indexing Using Minutia Detail and Delaunay Triangle

This paper is concentrated on an accurate and efficient fingerprint indexing algorithm, which efficiently retrieves the top N possibly matched candidates from a huge database. In order to have ability of coping with distorted fingerprints, the proposed algorithm uses novel features, which are insensitive to distortion, formed by the Delaunay triangulation of minutiae set as the representation unit. These features include minutia detail and Delaunay triangle (its handedness, angles, maximum edge, and related angle between orientation field and edges). Experiments on database FVC 2000 and scanned fingerprints with heavy distortion show our algorithm considerably narrows down the search space in fingerprint databases and is also available for distorted fingerprints. We also compared with other indexing approaches, and results show our algorithm has a better performance, especially on fingerprints with heavy distortion. This algorithm has another significant advantage that is it provides the control points for fingerprint distortion compensation.
A forward approach of constructing three-dimensional electromagnetic parametric scattering model based on geometrical model

This paper presents a forward approach to construct three-dimensional (3 D) electromagnetic parametric scattering model for a known complex radar target based on its geometrical CAD model. Similar to component disassembly method (CMD), we extract strong scattering source based on the components decomposition of complex target but fully considering the mutual coupling between the components, with reference to the existed parametric scattering models that describe the radar response of canonical shapes, we construct the parametric model. Then we obtain the value of the parameters through the theoretical solution and the genetic algorithm. We apply the approach to construct a parametric model of the S LICY model and simulation results demonstrate the effectiveness of the approach.
Mouse androgen‐dependent epididymal glycoprotein crisp‐1 (DE/AEG): Isolation, biochemical characterization, and expression in recombinant form

In the rat, the secretory glycoprotein DE/AEG is one of the main constitutents of the epididymal fluid. We have recently reported the cloning of the cDNA for the related cysteine‐rich secretory protein‐1 (CRISP‐1) from murine epididymis (Haendler et al., 1993; Endocrinology 133:192–198). The protein has now been isolated from the same organ and its N‐terminal amino acid sequence has been determined. CRISP‐1 exhibited an iso‐electric point of ∼6.8. High levels of CRISP‐1 antigen were detected in the corpus and cauda of the epididymis, vas deferens, seminal vesicle, prostate, and in the salivary gland by immunohistochemistry. A quantitative analysis of the cauda epididymal fluid by sandwich ELISA revealed that CRISP‐1 represented ∼15% of the total protein. For heterologous expression, the CRISP‐1 coding sequence was introduced into the pMPSV/CMV vector before transfection of baby hamster kidney (BHK) cells and selection with puromycin and neomycin. Expression in insect cells was achieved by co‐transfection of Sf9 cells with a transfer vector and baculovirus DNA. Recombinant CRISP‐1 was isolated in quantities sufficient for structural analysis. Ethyl maleimide treatment showed that all 16 cysteines were engaged in disulfide bonds. Proteolytic digestion demonstrated that the six cysteines localized in the N‐terminal moiety formed three bonds with each other, suggesting the existence of two discrete domains in the protein. © 1995 wiley‐Liss, Inc.
The effect of bias on the guesswork of hash functions

In this work we analyze the average guesswork for the problem of hashed password cracking (i.e., finding a password that has the same hash value as the actual password), when averaging over all hash functions whose effective distribution is i.i. d. Bernoulli(p) for any strategy of guessing passwords one by one (i.e., the fractions of passwords that are hashed to any bin, correspond to a probability mass function, which is i.i.d. Bernoulli(p)). We analyze the average guesswork under both online and offline attacks by deriving upper and lower bounds on the average guesswork as a function of the bins to which passwords are hashed, along with the most likely average guesswork, that is, the average guesswork of the most likely set of bins. Furthermore, we provide a concentration result that shows for this problem, that the probability mass function of guesswork is concentrated around its mean value. These results give quantifiable bounds for the effect of bias as well as the number of users on the average guesswork of a hash function, and show that increasing the number of users has a far worse effect than bias in terms of the average guesswork. However, when there exists a backdoor mechanism that enables “beamforming” certain passwords to the least likely bins, bias can in fact increase the average guesswork.
Dimension optimization of a planar 3-RRR parallel manipulator considering motion and force transmissibility

As the intrinsic characteristic of parallel manipulators, motion/force transmission performance has an extremely important influence on the performance of parallel robot systems. This study focuses on the evaluation of the motion/force transmission performance and dimensional optimization of a planar 3-RRR parallel manipulator by considering its motion/force transmissibility. An inverse kinematic analysis of the manipulator is presented. The local transmission index (LTI) of the manipulator is calculated, and two global design indices are defined based on the LTI for performance evaluation and dimensional synthesis. The process of optimal kinematic design of the manipulator based on performance charts is then presented. The optimized manipulator has a large workspace in area and shape, within which it has good motion/force transmissibility.
A Reinforcement-Learning Approach to Color Quantization

Color quantization is a process of sampling three-dimensional color space (e.g. RGB) to reduce the number of colors in a color image. By reducing to a discrete subset of colors known as a color codebook or palette, each pixel in the original image is mapped to an entry according to these palette colors. In this paper, a reinforcement-learning approach to color image quantization is proposed. Fuzzy rules, which are used to select appropriate parameters for the adaptive clustering algorithm applied to color quantization, are built through reinforcement learning. By comparing this new method with the original adaptive clustering algorithm on 30 color images, our method shows an improvement of 3.3% to 5.8% in peak signal to noise ratio (PSNR) values on average and results in savings of about 10% in computation time. Moreover, we demonstrate that reinforcement learning is an efficacious as well as efficient way to provide a solution of the learning problem where there is a lack of knowledge regarding the input-output relationship.
Soil Colloidal P Release Potentials under Various Polyacrylamide Addition Levels

Anionic polyacrylamide (PAM) can prevent soil erosion, but its effect on fine particulate phosphorus (P), such as colloidal P, has not been thoroughly examined. The effects of PAM on the release potentials of water‐dispersible colloids (WDC) and total P, molybdenum‐reactive P (MRP), and molybdenum‐unreactive P (MUP) in the colloidal and truly dissolved phases (i.e., TPcoll, MRPcoll, MUPcoll, TPtruly, MRPtruly, and MUPtruly) from six soils across South China were tested in this study. The results showed that the release potentials of TPcoll in the control treatments were 6·9–46·1 mg kg−1 and generally highest in sandy loam soil. Following low (12·5 kg ha−1), middle (25 kg ha−1), and high (50 kg ha−1) levels of PAM application, the release potential of TPcoll decreased by 41·7, 63·2, and 77·4% compared to the control group, respectively. Additionally, PAM may trigger MRPcoll and TPtruly releases in sandy loam and/or silt soils, and for most soils, MRPtruly and MUPtruly showed the highest release potentials at middle or high PAM levels. A significant PAM application level by soil site interaction for the release potentials of WDC and colloidal P was observed. Multiple linear regression showed that the PAM rate combined with soil sand content can successfully predict the release potentials of WDC (R2 = 0·552, p < 0·001) and TPcoll (R2 = 0·738, p < 0·001). Our results suggest that PAM can effectively reduce the loss of soil colloids and colloidal P, while its effects are related to both application level and soil texture. Copyright © 2017 John Wiley & Sons, Ltd.
Role of the PsbI Protein in Photosystem II Assembly and Repair in the Cyanobacterium Synechocystis sp. PCC 68031[W][OA]

The involvement of the PsbI protein in the assembly and repair of the photosystem II (PSII) complex has been studied in the cyanobacterium Synechocystis sp. PCC 6803. Analysis of PSII complexes in the wild-type strain showed that the PsbI protein was present in dimeric and monomeric core complexes, core complexes lacking CP43, and in reaction center complexes containing D1, D2, and cytochrome b-559. In addition, immunoprecipitation experiments and the use of a histidine-tagged derivative of PsbI have revealed the presence in the thylakoid membrane of assembly complexes containing PsbI and either the precursor or mature forms of D1. Analysis of PSII assembly in the psbI deletion mutant and in strains lacking PsbI together with other PSII subunits showed that PsbI was not required for formation of PSII reaction center complexes or core complexes, although levels of unassembled D1 were reduced in its absence. However, loss of PsbI led to a dramatic destabilization of CP43 binding within monomeric and dimeric PSII core complexes. Despite the close structural relationship between D1 and PsbI in the PSII complex, PsbI turned over much slower than D1, whereas high light-induced turnover of D1 was accelerated in the absence of PsbI. Overall, our results suggest that PsbI is an early assembly partner for D1 and that it plays a functional role in stabilizing the binding of CP43 in the PSII holoenzyme.
Why Transactional Memory Should Not Be Obstruction-Free

Transactional memory (TM) is an inherently optimistic abstraction: it allows concurrent processes to execute sequences of shared-data accesses (transactions) speculatively, with an option of aborting them in the future. Early TM designs avoided using locks and relied on non-blocking synchronization to ensure obstruction-freedom: a transaction that encounters no step contention is not allowed to abort. However, it was later observed that obstruction-free TMs perform poorly and, as a result, state-of-the-art TM implementations are nowadays blocking, allowing aborts because of data conflicts rather than step contention. In this paper, we explain this shift in the TM practice theoretically, via complexity bounds. We prove a few important lower bounds on obstruction-free TMs. Then we present a lock-based TM implementation that beats all of these lower bounds. In sum, our results exhibit a considerable complexity gap between non-blocking and blocking TM implementations.
Scheduling with Explorable Uncertainty

We introduce a novel model for scheduling with explorable uncertainty. In this model, the processing time of a job can potentially be reduced (by an a priori unknown amount) by testing the job. Testing a job $j$ takes one unit of time and may reduce its processing time from the given upper limit $\bar{p}_j$ (which is the time taken to execute the job if it is not tested) to any value between $0$ and $\bar{p}_j$. This setting is motivated e.g. by applications where a code optimizer can be run on a job before executing it. We consider the objective of minimizing the sum of completion times. All jobs are available from the start, but the reduction in their processing times as a result of testing is unknown, making this an online problem that is amenable to competitive analysis. The need to balance the time spent on tests and the time spent on job executions adds a novel flavor to the problem. We give the first and nearly tight lower and upper bounds on the competitive ratio for deterministic and randomized algorithms. We also show that minimizing the makespan is a considerably easier problem for which we give optimal deterministic and randomized online algorithms.
Exploiting Semantics and Speculation for Improving the Performance of Read-only Transactions

A read-only transaction (ROT) does not modify any data. Efforts are being made in the literature to improve the performance of ROTs without correctness and data currency issues. The widely used twophase locking protocol (2PL) processes the transactions without any correctness and data currency issues. However, the performance of 2PL deteriorates with data contention. Snapshot isolation (SI)-based protocols proposed in the literature improve the performance of ROTs, but they compromise on correctness and data currency issues. Speculative locking (SL) protocols are proposed in the literature for improving the performance of ROTs by carrying out speculative executions only for ROTs and following 2PL for update transactions. In SL-based protocols, update transactions are blocked if they conflicting with ROTs. In this paper, we have proposed an improved approach to improve parallelism among update transactions and ROTs by exploiting a new notion called “compensatability”. In this protocol, an ROT which can be “compensatable” can complete the execution and carry out compensating operation to incorporate the effect of conflicting update transactions. As a result, the parallelism is improved over SL protocols as the update transactions which are conflicting with ‘compensatable’ ROTs need not block. In this paper, we have proposed a protocol by exploiting both “compensatability” property of ROTs and speculation. The simulation results show that the proposed protocol improves the performance by carrying out less number of speculative executions. Further, the proposed protocol does not violate serializability criteria.