Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Fungal Keratitis using a Newly Developed Computer Program, Optscore, for Grading Digital Corneal Photographs

Abstract Purpose: To validate computer software developed to assess digital corneal photographs of fungal keratitis in clinical research. Methods: A cornea specialist and five medical students (after training) graded on two occasions 100 corneal photographs of patients with fungal keratitis using Optscore software. Variables assessed were lesion area, location, degree of opacity, percentage of the ulcer lying within a central 4 mm circle of the cornea. Intraclass correlation coefficients (ICCs) were used to assess intragrader reliability, agreement of the students with the corneal specialist, and the reliability of the group mean of the student raters. The area determined using Optscore was compared to the area estimated from slit lamp and to visual acuity. Results: As a group, medical students achieved an ICC greater than 0.9 for five out of the seven assessed variables. Similar levels of consistency were found after analyzing the graders’ individual results compared to the specialist. The area estimated using slit lamp examination was highly correlated with the mean area determined by Optscore, as was the logarithm of the minimum angle of resolution visual acuity at enrollment. Conclusions: Non-expert graders using Optscore to assess digital photographs of fungal keratitis are self-consistent, agree with an expert grader both as a group and individually, and measurements of ulcer area obtained from Optscore are highly correlated with measurements of the same patients obtained on clinical examination. These observations support the validity of Optscore for assessing corneal pathology associated with fungal keratitis and make it a promising clinical research tool.
From words to concepts in Text Mining

Text mining processes mostly employ the keyword searches where keywords are extracted from text or using standard thesauri. Key word employment depends on either detecting the significant content reflective words or high frequent words. However, the key word approaches do not ensure semantic retrieval as the confinement of concepts to words is away from reality. Keyword enhancement is applied using term weighting and relevancy ranking in some web processing and search systems. The strength and short comings of these approaches are reviewed in [1].
Can Shaker Potassium Channels be Locked in the Deactivated State?

For structural studies it would be useful to constrain the voltage sensor of a voltage-gated channel in its deactivated state. Here we consider one Shaker potassium channel mutant and speculate about others that might allow the channel to remain deactivated at zero membrane potential. Ionic and gating currents of F370C Shaker, expressed in Xenopus oocytes, were recorded in patches with internal application of the methanethiosulfonate reagent MTSET. It appears that the voltage dependence of voltage sensor movement is strongly shifted by reaction with internal MTSET, such that the voltage sensors appear to remain deactivated even at positive potentials. A disadvantage of this construct is that the rate of modification of voltage sensors by MTSET is quite low, ∼0.17 mM−1·s−1 at −80 mV, and is expected to be much lower at depolarized potentials.
Overland dispersal of aquatic invasive species: a risk assessment of transient recreational boating.

Predictions of the geographic spread of introduced species are often limited by a lack of data on their mechanisms of dispersal. We interviewed boaters and inspected boating equipment at public boat launches on Lake St. Clair (Michigan, USA) to assess the potential for the zebra mussel, an invasive bivalve, to be dispersed overland to inland waters by transient recreational boating activities. Several mechanisms associated with recreational boating were found to be capable of transporting either larval or adult life stages. Larvae were found in all forms of water carried by boats (i.e., in live wells, bilges, bait buckets, and engines) but were estimated to be 40–100× more abundant in live wells than other locations. Dilution in receiving waters should, however, greatly reduce the risk of establishing new populations by the introduction of larvae. Contrary to common belief, mussel dispersal from these boat launches did not occur by direct attachment to transient boats. Rather, adult and juvenile mussels were transported primarily on macrophytes entangled on boat trailers and, less frequently, on anchors (5.3% and 0.9% of departing boats, respectively). Combining these data with estimates of survival in air and reported boater destinations, we predict that a maximum of 0.12% of the trailered boats departing these access sites delivered live adult mussels to inland waters solely by transport on entangled macrophytes. While this is a small probability, high levels of vector activity resulted in a prediction of a total of 170 dispersal events to inland waters within the summer season from the primary boat launch studied. Many other potential vectors remain to be assessed, but the dispersal of zebra mussels by trailered boats, particularly by “piggybacking” on macrophytes entangled on the trailers, must be controlled in order to limit further range expansion of the zebra mussel within North America.
Helicobacter pylori infection and gastric lymphoma.

BACKGROUND Helicobacter pylori infection is a risk factor for gastric adenocarcinoma. We examined whether this infection is also a risk factor for primary gastric non-Hodgkin's lymphoma. METHODS This nested case-control study involved two large cohorts (230,593 participants). Serum had been collected from cohort members and stored, and all subjects were followed for cancer. Thirty-three patients with gastric non-Hodgkin's lymphoma were identified, and each was matched to four controls according to cohort, age, sex, and date of serum collection. For comparison, 31 patients with nongastric non-Hodgkin's lymphoma from one of the cohorts were evaluated, each of whom had been previously matched to 2 controls. Pathological reports and specimens were reviewed to confirm the histologic type of the tumor. Serum samples from all subjects were tested for H. pylori IgG by an enzyme-linked immunosorbent assay. RESULTS Thirty-three cases of gastric non-Hodgkin's lymphoma occurred a median of 14 years after serum collection. Patients with gastric lymphoma were significantly more likely than matched controls to have evidence of previous H. pylori infection (matched odds ratio, 6.3; 95 percent confidence interval, 2.0 to 19.9). The results were similar in both cohorts. Among the 31 patients with nongastric lymphoma, a median of six years had elapsed between serum collection and the development of disease. No association was found between nongastric non-Hodgkin's lymphoma and previous H. pylori infection (matched odds ratio, 1.2; 95 percent confidence interval, 0.5 to 3.0). CONCLUSIONS Non-Hodgkin's lymphoma affecting the stomach, but not other sites, is associated with previous H. pylori infection. A causative role for the organism is plausible, but remains unproved.
Phaseless Recovery Using the Gauss–Newton Method

In this paper, we propose a Gauss–Newton algorithm to recover an <inline-formula><tex-math notation="LaTeX">$ n$</tex-math></inline-formula>-dimensional signal from its phaseless measurements. The algorithm has two stages. In the first stage, the algorithm obtains a good initialization by calculating the eigenvector corresponding to the largest eigenvalue of a Hermitian matrix. In the second stage, the algorithm solves an optimization problem iteratively using the Gauss–Newton method. Our initialization method makes full use of all measurements and provides a good initial guess, as long as the number of random measurements is <inline-formula> <tex-math notation="LaTeX">$O(n)$</tex-math></inline-formula>. For real-valued signals, we prove that a resampled version of Gauss–Newton iterations converges to the global optimal solution quadratically with <inline-formula> <tex-math notation="LaTeX">$ O(n\log n)$</tex-math></inline-formula> random measurements. Numerical experiments show that the Gauss–Newton method has better empirical performance than other algorithms, such as the Wirtinger flow algorithm and Altmin phase algorithm.
The α3β3γ Subcomplex of the F1-ATPase from the Thermophilic Bacillus PS3 with the βT165S Substitution Does Not Entrap Inhibitory MgADP in a Catalytic Site during Turnover*

The hydrolytic properties of the mutant α3(βT165S)3γ and wild-type α3β3γ subcomplexes of TF1 have been compared. Whereas the wild-type complex hydrolyzes 50 μM ATP in three kinetic phases, the mutant complex hydrolyzes 50 μM ATP with a linear rate. After incubation with a slight excess of ADP in the presence of Mg2+, the wild-type complex hydrolyzes 2 mM ATP with a long lag. In contrast, prior incubation of the mutant complex under these conditions does not affect the kinetics of ATP hydrolysis. The ATPase activity of the wild-type complex is stimulated 4-fold by 0.1% lauryl dimethylamine oxide, whereas this concentration of lauryl dimethylamine oxide inhibits the mutant complex by 25%. Compared with the wild-type complex, the activity of the mutant complex is much less sensitive to turnover-dependent inhibition by azide. This comparison suggests that the mutant complex does not entrap substantial inhibitory MgADP in a catalytic site during turnover, which is supported by the following observations. ATP hydrolysis catalyzed by the wild-type complex is progressively inhibited by increasing concentrations of Mg2+ in the assay medium, whereas the mutant complex is insensitive to increasing concentrations of Mg2+. A Lineweaver-Burk plot constructed from rates of hydrolysis of 20-2000 μM ATP by the wild-type complex is biphasic, exhibiting apparent Km values of 30 μM and 470 μM with corresponding kcat values of 26 and 77 s−1. In contrast, a Lineweaver-Burk plot for the mutant complex is linear in this range of ATP concentration, displaying a Km of 133 μM and a kcat of 360 s−1.
Stroke and Circulating Extracellular RNAs

Background and Purpose— There is increasing interest in extracellular RNAs (ex-RNAs), with numerous reports of associations between selected microRNAs (miRNAs) and a variety of cardiovascular disease phenotypes. Previous studies of ex-RNAs in relation to risk for cardiovascular disease have investigated small numbers of patients and assayed only candidate miRNAs. No human studies have investigated links between novel ex-RNAs and stroke. Methods— We conducted unbiased next-generation sequencing using plasma from 40 participants of the FHS (Framingham Heart Study; Offspring Cohort Exam 8) followed by high-throughput polymerase chain reaction of 471 ex-RNAs. The reverse transcription quantitative polymerase chain reaction included 331 of the most abundant miRNAs, 43 small nucleolar RNAs, and 97 piwi-interacting RNAs in 2763 additional FHS participants and explored the relations of ex-RNAs and prevalent (n=63) and incident (n=51) stroke and coronary heart disease (prevalent=286, incident=69). Results— After adjustment for multiple cardiovascular disease risk factors, 7 ex-RNAs were associated with stroke prevalence or incidence; there were no ex-RNA associated with prevalent or incident coronary heart disease. Statistically significant ex-RNA associations with stroke were specific, with no overlap between prevalent and incident events. Conclusions— This is the largest study of ex-RNAs in relation to stroke using an unbiased approach in an observational cohort and the first large study to examine human small noncoding RNAs beyond miRNAs. These results demonstrate that when studied in a large observational cohort, extracellular miRNAs are associated with stroke risk.
An optimized ontology transfer learning method

Recently, more and more research is devoted for ontology in the semantic web domain. Firstly, a method for choosing the set of candidate similar concepts is presented based on ontology graphical structural features and data mining. Secondly, a calculation method of conceptual similarity is proposed based on the characteristics of the concept ontology and information content. Finally, the optimized ontology can be transferred into learning. Experimental results illustrate that this method is effective for computing the concept similarity and ontology can be transferred successfully to learn.
Formalizations of secrecy of encrypted databases against realistic attackers

Encrypted databases store data as ciphertexts. Encryption schemes with functionalities (such as deterministic and order-preserving schemes) are often used, in order to operate and compare the encrypted data directly. However, the secrecy of the data may decrease because information on plaintexts such as equivalence and order relationships are revealed from ciphertexts. In our previous study, we formalized secrecy against disclosure of ciphertexts in encrypted databases. The proposed secrecy is based on inference on databases: We simulate attacker's inference on specified secret information with and without the revealed information. When two inference results are the same, then secrecy of the specified information is regarded as preserved. However, this formalization does not capture how the secrecy decreases against realistic attackers, because computation power beyond probabilistic polynomial time is necessary for such inference. In this paper, we focus on the situation where a database instance is modeled as a sequence of tuples, rather than a set or a bag of tuples. Under this database model, we propose a formalization of the secrecy against realistic attackers with a probabilistic polynomial-time inference algorithm. The inference algorithm is derived naturally when the attackers infer on the encrypted databases with given information. Next, in order to make the formalization more general, we discuss secrecy against attackers who may use some auxiliary information depending on the database instance during inference. However, we prove that secrecy against such attackers cannot be achieved in the case where the entropy of the auxiliary information is not less than that of the sensitive information.
Part of Xenopus translin is localized in the centrosomes during mitosis.

During oogenesis, maternal mRNAs are synthesised and stored in a translationally dormant form due to the presence of regulatory elements at the 3' untranslated regions (3'UTR). In Xenopus oocytes, several studies have described the presence of RNA-binding proteins capable to repress maternal-mRNA translation. The testis-brain RNA-binding protein (TB-RBP/Translin) is a single-stranded DNA- and RNA-binding protein which can bind the 3' UTR regions (Y and H elements) of stored mRNAs and can suppress in vitro translation of the mRNAs that contain these sequences. Here we report the cloning of the Xenopus homologue of the TB-RBP/Translin protein (X-translin) as well as its expression, its localisation, and its biochemical association with the protein named Translin associated factor X (Trax) in Xenopus oocytes. The fact that this protein is highly present in the cytoplasm from stage VI oocytes until 48 h embryos and that it has been described as capable to inhibit paternal mRNA translation, indicates that it could play an important role in maternal mRNA translation control during Xenopus oogenesis and embryogenesis. Moreover, we investigated X-translin localisation during cell cycle in XTC cells. In interphase, although a weak and diffuse nuclear staining was observed, X-translin was mostly present in the cytoplasm where it exhibited a prominent granular staining. Interestingly, part of X-translin underwent a remarkable redistribution throughout mitosis and associated with centrosomes, which may suggest a new unknown role for this protein in cell cycle.
Sol-Gel Derived Li2O Doped BNT-BKT-BT Ceramics: Microstructure and Piezoelectric Properties

The introduction of lithium ion into BNT-BKT-BT ceramics with sol-gel method allows the development of high-performance lead-free piezoelectric ceramics. Nanoscale precursor powders were synthesized through calcination of amorphous gels, and densified ceramics with single perovskite structure were prepared at a relatively low sintering temperature 1110 °C. Crystal grain growth was fully developed with the Li+ addition through scanning electron microscope observation. Enhanced electrical properties, piezoelectric constant d33~184 pC/N and planar electromechanical coupling factor kp~0.30, were obtained for the ceramics.
A Freely Available Morphological Analyzer, Disambiguator and Context Sensitive Lemmatizer for German

In this paper we present Morphy, an integrated tool for German morphology, part-of-speech tagging and context-sensitive lemmatization. Its large lexicon of more than 320, 000 word forms plus its ability to process German compound nouns guarantee a wide morphological coverage. Syntactic ambiguities can be resolved with a standard statistical part-of-speech tagger. By using the output of the tagger, the lemmatizer can determine the correct root even for ambiguous word forms. The complete package is freely available and can be downloaded from the World Wide Web.
Modelling and control of an unmanned surface vehicle for environmental monitoring

: This paper presents an initial study of the autopilot development of an unmanned surface vehicle (USV). The USV named Springer is being developed to carry out pollutant tracking, and environmental and hydrographic surveys in rivers, reservoirs, inland waterways and coastal waters, particularly where shallow waters prevail. The catamaran shaped autonomous vessel is modelled as a two input, single output system whereas the autopilot selected is a genetic algorithm based model predictive controller (MPC). The USV dynamic model is obtained using system identiﬁcation techniques. Simulation results depicting the autopilot performance in response to changes in the desired course are demonstrated.
A self-acting thrust bearing for high speed micro-rotors

A self-pressurizing hydrodynamic thrust bearing has been designed, fabricated and tested up to speeds of 450,000 rpm on a 4.2 mm diameter MEMS radial inflow turbine. This test device demonstrated the load bearing capability predicted by the macro-scale gas bearing theory derived from the literature. The design of the devices tested was compromised to fit an existing geometry and fabrication sequence. Given more design freedom, these bearings should be capable of operating at several million rpm. Compared to existing hydrostatic thrust bearings, a hydrodynamic approach offers significantly simplified fabrication and elimination of the need for a source of pressurized gas external to the bearing.
The DNA methylation inhibitor induces telomere dysfunction and apoptosis of leukemia cells that is attenuated by telomerase over-expression

DNA methyltransferase inhibitors (DNMTIs) such as 5-azacytidine (5-AZA) have been used for treatment of acute myeloid leukemia (AML) and other malignancies. Although inhibiting global/gene-specific DNA methylation is widely accepted as a key mechanism behind DNMTI anti-tumor activity, other mechanisms are likely involved in DNMTI's action. Because telomerase reverse transcriptase (TERT) plays key roles in cancer through telomere elongation and telomere lengthening-independent activities, and TERT has been shown to confer chemo- or radio-resistance to cancer cells, we determine whether DNMTIs affect telomere function and whether TERT/telomerase interferes with their anti-cancer efficacy. We showed that 5-AZA induced DNA damage and telomere dysfunction in AML cell lines by demonstrating the presence of 53-BP1 foci and the co-localization of 53-BP1 foci with telomere signals, respectively. Telomere dysfunction was coupled with diminished TERT expression, shorter telomere and apoptosis in 5-AZA-treated cells. However, 5-AZA treatment did not lead to changes in the methylation status of subtelomere regions. Down-regulation of TERT expression similarly occurred in primary leukemic cells derived from AML patients exposed to 5-AZA. TERT over-expression significantly attenuated 5-AZA-mediated DNA damage, telomere dysfunction and apoptosis of AML cells. Collectively, 5-AZA mediates the down-regulation of TERT expression, and induces telomere dysfunction, which consequently exerts an anti-tumor activity.
Ad-hoc limited scale-free models for unstructured peer-to-peer networks

Several protocol efficiency metrics (e.g., scalability, search success rate, routing reachability and stability) depend on the capability of preserving structure even over the churn caused by the ad-hoc nodes joining or leaving the network. Preserving the structure becomes more prohibitive due to the distributed and potentially uncooperative nature of such networks, as in the peer-to-peer (P2P) networks. Thus, most practical solutions involve unstructured approaches while attempting to maintain the structure at various levels of protocol stack. The primary focus of this paper is to investigate construction and maintenance of scale-free topologies in a distributed manner without requiring global topology information at the time when nodes join or leave. We consider the uncooperative behavior of peers by limiting the number of neighbors to a pre-defined hard cutoff value (i.e., no peer is a major hub), and the ad-hoc behavior of peers by rewiring the neighbors of nodes leaving the network. We also investigate the effect of these hard cutoffs and rewiring of ad-hoc nodes on the P2P search efficiency.
Microarray-Based Transcriptomic Analysis of Differences between Long-Term Gregarious and Solitarious Desert Locusts

Desert locusts (Schistocerca gregaria) show an extreme form of phenotypic plasticity and can transform between a cryptic solitarious phase and a swarming gregarious phase. The two phases differ extensively in behavior, morphology and physiology but very little is known about the molecular basis of these differences. We used our recently generated Expressed Sequence Tag (EST) database derived from S. gregaria central nervous system (CNS) to design oligonucleotide microarrays and compare the expression of thousands of genes in the CNS of long-term gregarious and solitarious adult desert locusts. This identified 214 differentially expressed genes, of which 40% have been annotated to date. These include genes encoding proteins that are associated with CNS development and modeling, sensory perception, stress response and resistance, and fundamental cellular processes. Our microarray analysis has identified genes whose altered expression may enable locusts of either phase to deal with the different challenges they face. Genes for heat shock proteins and proteins which confer protection from infection were upregulated in gregarious locusts, which may allow them to respond to acute physiological challenges. By contrast the longer-lived solitarious locusts appear to be more strongly protected from the slowly accumulating effects of ageing by an upregulation of genes related to anti-oxidant systems, detoxification and anabolic renewal. Gregarious locusts also had a greater abundance of transcripts for proteins involved in sensory processing and in nervous system development and plasticity. Gregarious locusts live in a more complex sensory environment than solitarious locusts and may require a greater turnover of proteins involved in sensory transduction, and possibly greater neuronal plasticity.