Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleotide sequence and genome organization of tomato leaf curl geminivirus.

The genome of tomato leaf curl virus (TLCV) from Australia was cloned and its complete nucleotide sequence determined. It is a single circular ssDNA of 2766 nucleotides containing the consensus nonanucleotide sequence present in all geminiviruses. It has six open reading frames with an organization resembling that of certain other dicotyledonous plant-infecting monopartite geminiviruses, i.e. tomato yellow leaf curl and beet curly top viruses. The regulatory sequences present indicate a bidirectional mode of transcription. A dimeric TLCV DNA clone was constructed in a binary vector and used to agroinoculate three different host species. Typical virus infections were produced, confirming that the single DNA component is sufficient for infectivity.
Practicing Evidence-Based Stroke Medicine.

The practice of evidence-based medicine depends on several steps: a basic science derived understanding of disease pathophysiology, epidemiological research, and the results of well-conducted and appropriately analyzed randomized clinical trials (RCTs). The approval of new therapies by regulatory agencies is also based largely on RCT determination of the safety and therapeutic efficacy of drugs and devices. Once a new therapy is approved for use in clinical practice, clinicians typically begin to use it in a manner which mirrors the clinical trial design, for example, in the population for who risk and benefit have been established. It must be acknowledged that in the United States and in other countries, clinicians have leeway in their therapeutic decision making and it is not uncommon for therapies to be used for situations not tested in the RCTs that led to approval, the so-called off-label use. The off-label use of stroke-related therapies is relatively common, and we will consider the appropriateness of doing this in 3 common clinical scenarios. The relatively recent demonstration of the efficacy of thrombectomy within 6 hours of stroke onset in 6 well-conducted RCTs provides convincing evidence that this treatment is highly effective in improving functional outcome.1,2 These RCTs carefully selected patients with small-to-moderate ischemic cores, primarily by assessing the pretreatment Alberta Stroke Program Early CT Score (ASPECTS) on a noncontrast head CT, but computerized tomography perfusion (CTP) and diffusion-weighted magnetic resonance imaging were also acquired in some patients. In these trials, the median baseline ASPECTS score was 9, indicating a very small ischemic core and in 3 of the trials a baseline score of ≤5 was an exclusion. Even in MR CLEAN (Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands), a trial which did not specify an ASPECTS exclusion criterion, the …
Extended Architecture Analysis Description Language for Software Product Line Approach in Embedded Systems

Describing architecture variabilities explicitly and precisely is important in the software product line approach for software development since it helps product derivation as well as modeling and managing the variabilities. The SAE AADL is an industry standard architecture analysis and design language for the automotive community, which originally was not intended to be used for software product line. In this paper, we propose EAADL a software product line architecture description language for the automotive domain that extends the SAE AADL. By incorporating orthogonal variability model into it, EAADL offers traceability with requirement engineering as well as the implementation process that is essential in software product line engineering.
Impacts of Intermittent Water Supply on Water Quality in Two Palestinian Refugee Camps

We investigated the quality of treated drinking water in Aida Camp and Alazzah Camp, two Palestinian refugee camps in the West Bank. Water supply in the two camps is intermittent: Water deliveries are first stored in a centrally located community tank before being pumped through distribution networks to users, who then store the water in rooftop tanks. Between March 2016 and June 2017, we examined water quality within the distribution system in the camps, testing 520 samples in Aida Camp and 198 samples in Alazzah Camp for total coliforms, Escherichia coli (E. coli) bacteria, and residual chlorine. We observed deterioration in water quality in both camps, but the deterioration was more pronounced in Aida Camp where 2.5% of community-tank samples, 5.0% of network samples, and 10% of rooftop-tank samples contained one or more colonies (per 100 mL) of total coliform bacteria. In Alazzah Camp, 3.7% of community-tank samples, 2.5% of network samples, and 5% rooftop-tank samples contained one or more colonies (per 100 mL) of total coliform bacteria. E. coli was detected in two samples from Aida Camp and one sample from Alazzah Camp. In both camps, average residual chlorine concentrations were higher in the community tanks than in rooftop tanks. The main factor influencing water quality deterioration in rooftop tanks in Aida Camp appears to be air temperature. We recommend more systematic water testing in the camps and greater transparency in reporting test results to camp residents.
DNA sequence polymorphism within hominoid species exceeds the number of phylogenetically informative characters for a HOX2 locus.

Within- and between-species variability was examined in a noncoding 238-bp segment of the HOX2 cluster. DNA of 4-26 individuals of four species (Pongo pygmaeus, Pan troglodytes, Gorilla gorilla, and Homo sapiens) was PCR amplified and electrophoresed in a denaturing gradient gel to screen for variability. Coupled amplification and sequencing was used to determine the complete sequence for each of the different alleles identified, one each in humans and orangutans, two in chimpanzees, and four in gorillas. Maximum-parsimony methods were used to construct a gene tree for these sequences. Alleles in all four species cluster into groups consisting of only one species (i.e., alleles within a species are monophyletic). The number of base-pair differences observed among alleles within P. troglodytes and within G. gorilla is larger than the number of base-pair substitutions that phylogenetically link Pan with Homo. Given these and other published data, it is premature to accept any particular phylogenetic tree that relates these three genera through two separate speciation events.
Recent Advances in Anti-Angiogenic Therapy of Cancer

Since angiogenesis is critical for tumor growth and metastasis, anti-angiogenic treatment is a highly promising therapeutic approach. Thus, for over last couple of decades, there has been a robust activity aimed towards the discovery of angiogenesis inhibitors. More than forty anti-angiogenic drugs are being tested in clinical trials all over the world. This review discusses agents that have approved by the FDA and are currently in use for treating patients either as single-agents or in combination with other chemotherapeutic agents.
Dimensional changes in acid-demineralized dentin matrices following the use of HEMA-water versus HEMA-alcohol primers.

Although dried acid-etched dentin can be reexpanded by hydroxyethyl methacrylate (HEMA)/water primers, the primed dentin collapses when the water is evaporated. Experimental HEMA/alcohol primers should stiffen the matrix and permit less shrinkage when the solvent is evaporated. The purpose of this study was to test the hypotheses that matrix shrinkage induced by solvent evaporation from HEMA primers is inversely related to solvent-induced matrix stiffness. Dentine discs were prepared from midcoronal dentine of unerupted human third molars. After demineralization in 37% phosphoric acid, the specimens were placed in the well of a linear variable differential transformer instrument, which measures changes in the matrix height and stiffness by load displacement after the application of weights. This was done in their hydrated state after water had been applied, after drying with dry nitrogen gas, and after the application of 35 vol % HEMA-water, HEMA-methanol, HEMA-ethanol, or HEMA-propanol primers. The degree of reexpansion after the application of the primers to the dentine in the dried state was found to be highest using the HEMA-water primer, followed by HEMA-methanol and HEMA-ethanol, with the HEMA-propanol primer producing no expansion. However, when the solvents were evaporated the HEMA-water-treated specimens shrank the most, the HEMA-ethanol-treated specimens shrank an intermediate amount, and the HEMA-methanol-treated specimens shrank the least. The net result of expansion minus shrinkage produced by evaporation determines how much HEMA remains in the hybrid layer just prior to polymerization.
Analysis of the Mobility of Signaling Molecules in Lymphocytes Using Fluorescence Photobleaching Techniques

The earliest biochemical events at the plasma membrane that lead to gene activation appear to depend not only on the local concentration of signaling molecules, but also on the mobility of these molecules at the site of signaling. To elucidate the process of signal transduction after receptor engagement in the immune system, it is important to analyze the mobility of signaling molecules in living lymphocytes. Current knowledge of the changes in intracellular localization and dynamic movements of signaling molecules during lymphocyte activation is limited. Here, we describe a method for known as fluorescence recovery after photobleaching, used to measure the diffusion mobility of a signaling molecule in a T cell line after T cell receptor stimulation. This method is a useful tool in studies of spatiotemporal regulation in immunoreceptor signaling.
Face Blurring for Privacy in Street-level Geoviewers Combining Face, Body and Skin Detectors

In the last two years, web-based applications using street-level images have been developing fast. In that context, privacy preservation is an unavoidable issue. We present in this paper a multi-boosting based approach to detect pedestrians in high resolution panoramics in order to blur their faces. This task is quite complex since these features vary in size, shape, color, and often are partially occluded, sometimes behind windows or inside cars, etc. Our strategy is thus based on the combination of two existing boosting algorithms detecting faces [1] and bodies [2] with a skin tone detection algorithm we developed. The results are quite encouraging for such an unconstrained data: 86.2% of true positives and an average of 2 false positive detections per image (2.1 MPixels). This combination solution provides much more robust results than each detection algorithm performed independently.
Carriers of the Complex Allele HFE c.[187C>G;340+4T>C] Have Increased Risk of Iron Overload in São Miguel Island Population (Azores, Portugal)

Iron overload is associated with acquired and genetic conditions, the most common being hereditary hemochromatosis (HH) type-I, caused by HFE mutations. Here, we conducted a hospital-based case-control study of 41 patients from the São Miguel Island (Azores, Portugal), six belonging to a family with HH type-I pseudodominant inheritance, and 35 unrelated individuals fulfilling the biochemical criteria of iron overload compatible with HH type-I. For this purpose, we analyzed the most common HFE mutations– c.845G>A [p.Cys282Tyr], c.187C>G [p.His63Asp], and c.193A>T [p.Ser65Cys]. Results revealed that the family’s HH pseudodominant pattern is due to consanguineous marriage of HFE-c.845G>A carriers, and to marriage with a genetically unrelated spouse that is a -c.187G carrier. Regarding unrelated patients, six were homozygous for c.845A, and three were c.845A/c.187G compound heterozygous. We then performed sequencing of HFE exons 2, 4, 5 and their intron-flanking regions. No other mutations were observed, but we identified the -c.340+4C [IVS2+4C] splice variant in 26 (74.3%) patients. Functionally, the c.340+4C may generate alternative splicing by HFE exon 2 skipping and consequently, a protein missing the α1-domain essential for HFE/ transferrin receptor-1 interactions. Finally, we investigated HFE mutations configuration with iron overload by determining haplotypes and genotypic profiles. Results evidenced that carriers of HFE-c.187G allele also carry -c.340+4C, suggesting in-cis configuration. This data is corroborated by the association analysis where carriers of the complex allele HFE-c. [187C>G;340+4T>C] have an increased iron overload risk (RR = 2.08, 95% CI = 1.40−2.94, p<0.001). Therefore, homozygous for this complex allele are at risk of having iron overload because they will produce two altered proteins—the p.63Asp [c.187G], and the protein lacking 88 amino acids encoded by exon 2. In summary, we provide evidence that the complex allele HFE-c. [187C>G;340+4T>C] has a role, as genetic predisposition factor, on iron overload in the São Miguel population. Independent replication studies in other populations are needed to confirm this association.
A lung cancer outcome calculator using ensemble data mining on SEER data

We analyze the lung cancer data available from the SEER program with the aim of developing accurate survival prediction models for lung cancer using data mining techniques. Carefully designed preprocessing steps resulted in removal/modification/splitting of several attributes, and 2 of the 11 derived attributes were found to have significant predictive power. Several data mining classification techniques were used on the preprocessed data along with various data mining optimizations and validations. In our experiments, ensemble voting of five decision tree based classifiers and meta-classifiers was found to result in the best prediction performance in terms of accuracy and area under the ROC curve. Further, we have developed an on-line lung cancer outcome calculator for estimating risk of mortality after 6 months, 9 months, 1 year, 2 year, and 5 years of diagnosis, for which a smaller non-redundant subset of 13 attributes was carefully selected using attribute selection techniques, while trying to retain the predictive power of the original set of attributes. The on-line lung cancer outcome calculator developed as a result of this study is available at http://info.eecs. northwestern.edu:8080/LungCancerOutcome-Calculator/
Mutations in NOD2 are associated with fibrostenosing disease in patients with Crohn's disease.

BACKGROUND & AIMS The clinical manifestations of Crohn's disease (CD) are diverse, ranging from fibrostenosing small-bowel disease to colon-predominant inflammation. These distinctions may represent genetic, immunologic, and microbial heterogeneity. NOD2 gene mutations in CD have been described recently and may alter innate immune responses. We hypothesized that NOD2 mutations may be associated with distinct phenotypic expressions of CD. METHODS Two cohorts of consecutively identified patients referred to an inflammatory bowel disease center (n = 142 collected between 1993 and 1996; n = 59 collected between 1999 and 2001) were genotyped for 3 single nucleotide variants of NOD2-R675W, G881R, and 3020insC-and phenotyped for disease behavior, disease location, and serum immune markers. RESULTS Univariate analysis showed that CD-associated NOD2 variants were significantly associated with fibrostenosing disease in each cohort (P = 0.049 and P = 0.002, respectively). When both cohorts were analyzed together, the association between NOD2 variants and fibrostenosing disease was more significant (P = 0.001). These relationships were observed in both Jews and non-Jews. Forty-six percent of patients with fibrostenosing disease carried at least 1 of these alleles, compared with only 23.5% of patients without fibrostenosing disease (odds ratio, 2.8; 95% confidence interval, 1.6-5.2). Multivariate and conditioning analyses showed a primary association between NOD2 allelic variants and fibrostenosing disease, but not with small-bowel disease. CONCLUSIONS In this description of a genotype/phenotype correlation in CD patients and NOD2 variants, data suggest that variation in this gene contributes to the occurrence of fibrostenotic CD of the small bowel.
Designing vaccines to prevent breast cancer recurrence or invasive disease.

With the emerging importance of the tumor immune environment in both invasive and preinvasive breast cancer, vaccine therapy may provide a well-tolerated, durable therapy for preinvasive breast cancer by preventing both recurrent preinvasive disease and progression to invasive disease. Preinvasive breast cancer is ideal for vaccines because the disease is slow growing and the patients are not immunosuppressed. However, design of the vaccines are critical including consideration of appropriate antigens, selecting Th1 stimulating epitopes, and using multiantigen vaccines to address tumor heterogeneity.
Utilization of fractionated soluble egg antigens reveals selectively modulated granulomatous and lymphokine responses during murine schistosomiasis mansoni

Worm eggs deposited in the livers and intestines of Schistosoma mansoni-infected mice secrete soluble egg antigens (SEA) and induce T cell-mediated circumoval granulomas. In the present study, we fractionated crude SEA by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and tested the fractions for granuloma elicitation and lymphokine production at different stages of the infection. SEA fraction-coupled beads were used to elicit artificial pulmonary granulomas. Acutely infected mice responded with granulomas to seven fractions (less than 21-, 25- to 30-, 32- to 38-, 60- to 66-, 70- to 90-, 93- to 125-, and greater than 200-kDa fractions) of SEA, whereas chronically infected mice responded to four fractions (60- to 66-, 70- to 90-, 93- to 125-, and greater than 200-kDa fractions). In response to both crude and fractionated SEA, granuloma T cells produced high levels of gamma interferon at the preacute (6-week) stage of infection, but production subsequently diminished. Interleukin-2 (IL-2) and IL-4 production peaked at the acute (8-week) stage of infection and concurrently decreased at the chronic (20-week) stage. At the acute stage of the infection, the granulomagenic SEA fractions also elicited IL-2 and IL-4 production; at the chronic stage, IL-2 production and, to a lesser degree, IL-4 production corresponded to SEA fractions that elicited granulomas. Isolated SEA proteins from the 32- to 38-kDa fraction demonstrated differential lymphokine responses: predominant gamma interferon and IL-2 production was elicited by the 32-kDa fraction, whereas the 35- and 38-kDa proteins elicited predominant gamma interferon and IL-4 production. However, all three proteins elicited granuloma formation. The present study reveals changes in granulomatous responses to SEA fractions during the acute and chronic stages of the infection as well as distinct phases of gamma interferon, IL-2, and IL-4 lymphokine production throughout the infection. Based on these results, it is concluded that granuloma formation and IL-2 and IL-4 production are interrelated.
OCaml + XDuce

This paper presents the core type system and type inference algorithm of OCamlDuce, a merger between OCaml and XDuce. The challenge was to combine two type checkers of very different natures while preserving the best properties of both (principality and automatic type reconstruction on one side; very precise types and implicit subtyping on the other side). Type inference can be described by two successive passes: the first one is an ML-like unification-based algorithm which also extracts data flow constraints about XML values; the second one is an XDuce-like algorithm which computes XML types in a direct way. An optional preprocessing pass, called strengthening, can be added to allow more implicit use of XML subtyping. This pass is also very similar to an ML type checker.
1 Randomized Time Complexity 1 . 1 How Large is BPP ?

We currently do not have a very good unconditional bound on the power of BPP — in particular, it could be that BPP = NEXP. Perhaps surprisingly, especially in light of the many randomized algorithms known, the current conjecture is that BPP is not more powerful than P. We will return to this point later in the semester when we talk about derandomization. What (unconditional) upper bounds can we place on BPP? Interestingly, we know that it is not more powerful than polynomial-size circuits; actually, the following theorem is also a good illustration of the power of non-uniformity.
Measuring the solar meridional flow from perturbations of eigenfunctions of global oscillations

We present a new concept to infer the meridional flow in the deep solar interior from global oscillation data. This concept is based on the estimation of the coupling strengths of p-mode eigenfunctions mediated by the meridional flow. We illustrate the performance of the method using simulations and present first inversion results of a large-scale flow component of the meridional flow obtained from MDI data.
CSBD: A Nonlinear Clustering Method Based on Cluster Shrinking and Border Detection

Nonlinear clustering has attracted an increasing amount of attention recently. In this paper, we propose a new nonlinear clustering method based on Cluster Shrinking and Border Detection (CSBD). Unlike most existing clustering method, the CSBD method focuses on every data point rather then the cluster centers. A novel idea, namely Cluster Shrinking, is designed to transform the original nonlinear datasets into several hyperspheres, which makes clustering work much easier. Besides, we also introduce a simple but effective Border Detection method based on histogram analysis to automatically determine the threshold parameter in Cluster Shrinking phase. Extensive experiments have been conducted to demonstrate the effectiveness of CSBD in both synthetic and real-world datasets.
PRIMA-1MET Inhibits Growth of Mouse Tumors Carrying Mutant p53

Reactivation of the tumor suppressor activity to mutant p53 should trigger massive apoptosis and eliminate tumors. The low molecular weight compounds PRIMA-1 and the structural analog PRIMA-1MET reactivate human mutant p53 in vitro and suppress growth of human tumor xenografts in SCID mice. However, little is known about their effect on mouse mutant p53 in mouse tumor cells. We have examined the effect of PRIMA-1MET on mouse sarcomas, mammary carcinomas and chemically induced fibrosarcomas. PRIMA-1MET showed potent growth suppression in mutant p53-carrying mouse tumors in vitro and a significant anti-tumor effect in syngeneic mice in vivo. These results demonstrate that PRIMA-1MET targets mouse tumors carrying mutant p53 and provide strong support for the anti-tumor efficiency of PRIMA-1METin vivo.
Spatial Spectrum Access Game

A key feature of wireless communications is the spatial reuse. However, the spatial aspect is not yet well understood for the purpose of designing efficient spectrum sharing mechanisms. In this paper, we propose a framework of spatial spectrum access games on directed interference graphs, which can model quite general interference relationship with spatial reuse in wireless networks. We show that a pure Nash equilibrium exists for the two classes of games: (1) any spatial spectrum access games on directed acyclic graphs, and (2) any games satisfying the congestion property on directed trees and directed forests. Under mild technical conditions, the spatial spectrum access games with random backoff and Aloha channel contention mechanisms on undirected graphs also have a pure Nash equilibrium. We also quantify the price of anarchy of the spatial spectrum access game. We then propose a distributed learning algorithm, which only utilizes users' local observations to adaptively adjust the spectrum access strategies. We show that the distributed learning algorithm can converge to an approximate mixed-strategy Nash equilibrium for any spatial spectrum access games. Numerical results demonstrate that the distributed learning algorithm achieves up to 100 percent performance improvement over a random access algorithm.