Miracle-dz/UniFAR-FTUs huggingface dataset:
The Cross-Talk between Spirochetal Lipoproteins and Immunity

Spirochetal diseases such as syphilis, Lyme disease, and leptospirosis are major threats to public health. However, the immunopathogenesis of these diseases has not been fully elucidated. Spirochetes interact with the host through various structural components such as lipopolysaccharides (LPS), surface lipoproteins, and glycolipids. Although spirochetal antigens such as LPS and glycolipids may contribute to the inflammatory response during spirochetal infections, spirochetes such as Treponema pallidum and Borrelia burgdorferi lack LPS. Lipoproteins are most abundant proteins that are expressed in all spirochetes and often determine how spirochetes interact with their environment. Lipoproteins are pro-inflammatory, may regulate responses from both innate and adaptive immunity and enable the spirochetes to adhere to the host or the tick midgut or to evade the immune system. However, most of the spirochetal lipoproteins have unknown function. Herein, the immunomodulatory effects of spirochetal lipoproteins are reviewed and are grouped into two main categories: effects related to immune evasion and effects related to immune activation. Understanding lipoprotein-induced immunomodulation will aid in elucidating innate immunopathogenesis processes and subsequent adaptive mechanisms potentially relevant to spirochetal disease vaccine development and to inflammatory events associated with spirochetal diseases.
Efficient and Accurate Local Learning for Ranking

Learning to score—and thereby order—items represented as feature vectors xi ∈ R, with the goal of minimizing various ranking loss functions, is now a major topic in Information Retrieval. Training data consists of relevant and irrelevant documents identified for a number of queries. Many systems train a model w ∈ R, such that the score of an item xi is wxi. However, queries are diverse: navigational, informational, transactional, etc. Recently, there has been interest in local learning: customizing a model to each test query. While intuitively appealing, these proposals have either resulted in modest gains, or entail excessive computational burden at test time. In this paper we propose a local learning algorithm based on a new similarity measure between queries. The proposed local learning algorithm does not depend on a fixed query classification scheme. First, we represent (relevant and irrelevant) document vectors for the query as a point cloud. Second, we define an intuitive notion of similarity between the shapes of two point clouds, based on principal component analysis (PCA). Our local learning algorithm clusters queries at training time, using the PCA-based measure of query similarity. During test time, we simply locate the nearest training cluster, and use the model trained for that cluster. Very few clusters are adequate to give substantial boost to test accuracy. Our test time is small, training time is reasonable, and our accuracy beats several recent local learning approaches, as tested on the well-known LETOR dataset.
Active Learning with Support Vector Machine Applied to Gene Expression Data for Cancer Classification

There is growing interest in the application of machine learning techniques in bioinformatics. The supervised machine learning approach has been widely applied to bioinformatics and gained a lot of success in this research area. With this learning approach researchers first develop a large training set, which is a time-consuming and costly process. Moreover, the proportion of the positive examples and negative examples in the training set may not represent the real-world data distribution, which causes concept drift. Active learning avoids these problems. Unlike most conventional learning methods where the training set used to derive the model remains static, the classifier can actively choose the training data and the size of training set increases. We introduced an algorithm for performing active learning with support vector machine and applied the algorithm to gene expression profiles of colon cancer, lung cancer, and prostate cancer samples. We compared the classification performance of active learning with that of passive learning. The results showed that employing the active learning method can achieve high accuracy and significantly reduce the need for labeled training instances. For lung cancer classification, to achieve 96% of the total positives, only 31 labeled examples were needed in active learning whereas in passive learning 174 labeled examples were required. That meant over 82% reduction was realized by active learning. In active learning the areas under the receiver operating characteristic (ROC) curves were over 0.81, while in passive learning the areas under the ROC curves were below 0.50.
Low-complexity zero-forcing coordinated beamforming by adaptive-perturbation for multi-cell MIMO networks

In this paper, an adaptive coordinated zero-forcing beamforming scheme based on null space perturbation is proposed for eliminating the inter-cell interference in multi-cell MIMO networks. The scheme makes use of the time-correlation of the channel response to reduce the number of times of singular-value-decomposition of channel matrix for zero-forcing coordinated beamforming. We also analyze the specific rate loss resulting from null space perturbation theoretically and present the method to set up the perturbation step length of different base stations according to the interference strength of a specific user. The simulation results show that the proposed algorithm can effectively reduce the algorithm complexity and obtain a significant performance enhancement compared to the algorithm with fixed perturbation step length.
Flash Reliability in Production: The Expected and the Unexpected

As solid state drives based on flash technology are becoming a staple for persistent data storage in data centers, it is important to understand their reliability characteristics. While there is a large body of work based on experiments with individual flash chips in a controlled lab environment under synthetic workloads, there is a dearth of information on their behavior in the field. This paper provides a large-scale field study covering many millions of drive days, ten different drive models, different flash technologies (MLC, eMLC, SLC) over 6 years of production use in Google's data centers. We study a wide range of reliability characteristics and come to a number of unexpected conclusions. For example, raw bit error rates (RBER) grow at a much slower rate with wearout than the exponential rate commonly assumed and, more importantly, they are not predictive of uncorrectable errors or other error modes. The widely used metric UBER (uncorrectable bit error rate) is not a meaningful metric, since we see no correlation between the number of reads and the number of uncorrectable errors. We see no evidence that higher-end SLC drives are more reliable than MLC drives within typical drive lifetimes. Comparing with traditional hard disk drives, flash drives have a significantly lower replacement rate in the field, however, they have a higher rate of uncorrectable errors.
Dynamic Load Balancing on Web-Server Systems

Popular Web sites cannot rely on a single powerful server nor on independent mirrored-servers to support the ever-increasing request load. Distributed Web server architectures that transparently schedule client requests offer a way to meet dynamic scalability and availability requirements. The authors review the state of the art in load balancing techniques on distributed Web-server systems, and analyze the efficiencies and limitations of the various approaches.
Donepezil Significantly Improves Abilities in Daily Lives of Female down Syndrome Patients with Severe Cognitive Impairment: A 24-Week Randomized, Double-Blind, Placebo-Controlled Trial

Objective: Down syndrome (DS) patients share certain neuropathological features with Alzheimer disease patients. A randomized, double-blind, placebo-controlled study was performed to investigate the efficacy and safety of donepezil, an Alzheimer disease drug, for DS patients. Method: Twenty-one DS patients with severe cognitive impairment were assigned to take donepezil (3 mg daily) or a placebo for 24 weeks, and evaluated for activities in daily lives by concisely modified International Classification of Functioning, Disability and Health (ICF) scaling system. Results: ICF scores significantly increased without any adverse effects in the donepezil group in comparison to those in the placebo control. Among the individual functions tested, there was a dramatic improvement in the global mental functions and in specific mental functions. Conclusions: Donepezil may effectively and safely improve overall functioning of DS patients with severe cognitive impairment.
Isozyme variation in Simulium (Edwardsellum) damnosum s.l. (Diptera: Simuliidae) from Kenya.

Isozyme variation of the Simulium damnosum sibling species complex was studied by cellulose acetate electrophoresis (CAE) from four Kenyan river systems. Two enzymes, PGM and HK, were diagnostic and differentiated the larvae collected in Western and Nyanza provinces from the larvae collected at Mt. Kenya. Allele frequency differences of the enzyme PGI allowed about 75% separation of the geographically distinct populations.
Hierarchical Reinforcement Learning and Safe State Abstraction on Realtime Strategy Games

For an agent to perform well in a dynamic environment, such as those in computer games, adaptation is required. However, the agents in the current games are scripted, which means they will not learn from experience and therefore do not adapt. Because of this lack of learning and adapting, it makes the current agents boring to play against as a human being. This paper presents a non scripted, non reactive approach to a simplified real time strategy game, using Hierarchical Reinforcement Learning, in particular the MaxQ method with safe state abstraction [1]. We will compare it to a Qlearning algorithm and MaxQ without safe state abstraction.
Progress towards development and adoption of integrated management systems against flystrike and lice in sheep

Ectoparasites of sheep, principally blowflies and lice, cost the New Zealand farming industry an estimated $60 million each year. This figure includes the cost of chemicals and labour used to treat or prevent flystrike and lice, together with the lost production. An Integrated Pest Management (IPM) trial project involving four groups of farmers (overall total 15) in four regions of New Zealand has been set up with the aim of adopting a holistic approach to managing these parasites and already early benefits have accrued to the farmers involved. Procedures were set up to reduce insecticide residues in wool by using techniques such as jetting which apply less chemical to the sheep but target it more appropriately and maintain or improve protection against flystrike and control of lice. As a consequence, savings in chemical and labour costs have been made. On two farms in particular, savings on these items ranged from $578 (27% reduction) on a property with 2000 Corriedale ewes to $3608 (52% reduction) on the other property with 8000 Romney ewes. An understanding that clean, healthy sheep, free of nematodes and dags, are less susceptible to flystrike and lice has also assisted in controlling the diseases. This paper also discusses the potential for biological control against blowfly populations, with large fly traps, sterilising baits and parasitoid wasps all being investigated. Research continues on specialist pastures such as birdsfoot trefoil (Lotus corniculatus) and sulla (Hedysarum coronarium) to evaluate the practicalities of incorporating their use in management systems for both nematode and flystrike control.
Functional Diversity of Plant–Pollinator Interaction Webs Enhances the Persistence of Plant Communities

Pollination is exclusively or mainly animal mediated for 70% to 90% of angiosperm species. Thus, pollinators provide an essential ecosystem service to humankind. However, the impact of human-induced biodiversity loss on the functioning of plant–pollinator interactions has not been tested experimentally. To understand how plant communities respond to diversity changes in their pollinating fauna, we manipulated the functional diversity of both plants and pollinators under natural conditions. Increasing the functional diversity of both plants and pollinators led to the recruitment of more diverse plant communities. After two years the plant communities pollinated by the most functionally diverse pollinator assemblage contained about 50% more plant species than did plant communities pollinated by less-diverse pollinator assemblages. Moreover, the positive effect of functional diversity was explained by a complementarity between functional groups of pollinators and plants. Thus, the functional diversity of pollination networks may be critical to ecosystem sustainability.
Th22 Cells as Well as Th17 Cells Expand Differentially in Patients with Early-Stage and Late-Stage Myelodysplastic Syndrome

Background Immunological mechanisms are increasingly recognized in the progression of myelodysplastic syndrome (MDS). Early-stage MDS (E-MDS) is characterized by autoimmune-mediated myelosuppression whereas late-stage MDS (L-MDS) involves immune evasion, giving dysplastic cells growth potential to progress into acute myeloid leukemia. T-helper (Th) 22 is involved in the pathogenesis of inflammatory autoimmunity and tumorigenesis. The roles of Th22 cells in the pathophysiology of E-MDS and L-MDS remain unsettled. Design and Methods We studied 37 MDS patients (E-MDS, n = 17; L-MDS, n = 20) and 20 healthy controls to characterize their peripheral blood (PB), as well as 25 MDS patients and 10 healthy controls to characterize their bone marrow(BM). The expression of Interleukin-22 (IL-22), IL-17 or interferon gamma (IFN-γ) was examined in E-MDS, L-MDS patients and controls by flow cytometry. The mRNA expression levels of RAR-related orphan receptor C (RORC), IL-6, tumor necrosis factor alpha (TNF-α) and IL-23 in peripheral blood mononuclear cells (PBMCs) were determined by real-time quantitative polymerase chain reaction. The levels of IL-22 and IL-17 both in PB and BM plasma were examined by enzyme-linked immunosorbent assay. Results In E-MDS, peripheral Th17 cells were significantly elevated and correlated with peripheral Th22 cells compared with healthy controls and L-MDS. Significantly higher levels of peripheral Th22 expansion, mRNA expression of IL-6, TNF-α and lower level of RORC mRNA expression were observed in L-MDS compared with E-MDS. No statistical difference was found in IL-23 mRNA expression or plasma IL-22, IL-17 levels among E-MDS, L-MDS and controls. Conclusions Our data demonstrated that L-MDS cohort had increased frequencies of peripheral Th22 cells and higher mRNA expression levels of IL-6 and TNF-α, indicating that Th22 cells along with Th17 cells or not are involved in the dynamic immune responses of MDS.
Effects of Hsp70.1 Gene Knockout on the Mitochondrial Apoptotic Pathway After Focal Cerebral Ischemia

Background and Purpose— Murine heat-shock protein 70 (HSP70) protein, which is produced from 2 genes, hsp70.1 and hsp70.3, is known to protect the brain against ischemic injury. However, little information is available on the antiapoptotic mechanism of HSP70.1 protein after cerebral ischemia. To evaluate the role of HSP70.1 protein in ischemia, we analyzed the mitochondrial apoptotic pathway using hsp70.1 knockout (KO) mice and their wild-type (WT) mice. Methods— hsp70.1 KO and WT mice underwent focal ischemia for 120 minutes. DNA fragmentation was evaluated by TUNEL staining. Cytochrome c release and the activation of caspase-3 were analyzed by Western blotting and immunohistochemistry. Results— hsp70.1 mRNA was not detected in hsp70.1 KO mice after ischemia, and HSP70 protein expression was markedly suppressed versus WT mice. KO mice showed a significantly greater infarction volume and DNA fragmentation in the cortex than WT mice at 24 hours after ischemia. At 8 hours, cytochrome c release into the cytoplasm was markedly higher in KO mice than in WT mice. Caspase-3 activation was also significantly enhanced in KO mice versus WT mice, as evidenced by higher levels of activated caspase-3 and cleaved gelsolin. Conclusions— These findings suggest that the deletion of the hsp70.1 gene increases cytochrome c release into the cytoplasm and subsequent caspase-3 activation, thereby exacerbating apoptosis after focal cerebral ischemia.
0.5 Gigapixel Microscopy Using a Flatbed Scanner References and Links 1. M. Oheim, " Advances and Challenges in High-throughput Microscopy for Live-cell Subcellular Imaging, " Expert

The capability to perform high-resolution, wide field-of-view (FOV) microscopy imaging is highly sought after in biomedical applications. In this paper, we report a wide FOV microscopy system that uses a closed-circuit-television (CCTV) lens for image relay and a flatbed scanner for data acquisition. We show that such an imaging system is capable of capturing a 10 mm × 7.5 mm FOV image with 0.78 µm resolution, resulting in more than 0.5 billion pixels across the entire image. The resolution and field curve of the proposed system were characterized by imaging a USAF resolution target and a hole-array target. To demonstrate its application, 0.5 gigapixel images of histology slides were acquired using this system. Space-bandwidth product of optical signals and systems, " J. Primary histologic diagnosis using automated whole slide imaging: a validation study, " BMC Clin. The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM), " Proc. Lensfree on-chip microscopy over a wide field-of-view using pixel super-resolution, " Opt. Increased space-bandwidth product in pixel super-resolved lensfree on-chip microscopy, " Sci. Toward giga-pixel nanoscopy on a chip: a computational wide-field look at the nano-scale without the use of lenses, " Wide field-of-view microscope based on holographic focus grid illumination, " Opt. Focal plane tuning in wide-field-of-view microscope with Talbot pattern illumination, " Opt. Wide field-of-view Talbot grid-based microscopy for multicolor fluorescence imaging, " Opt. High resolution digital holographic microscopy with a wide field of view based on a synthetic aperture technique and use of linear CCD scanning, " Appl. Quantitative phase imaging via Fourier ptychographic microscopy, " Opt. A 3mpixel multi-aperture image sensor with 0.7 um pixels in 0.11 um cmos, " in IEEE ISSCC Digest of Technical Papers 48–49 (2008). 18. M. Ben-Ezra, " A digital gigapixel large-format tile-scan camera, " IEEE Comput. Characterization of spatially varying aberrations for wide field-of-view microscopy, " Opt.
Maternal and nenonatal tenofovir and emtricitabine to prevent vertical transmission of HIV-1: tolerance and resistance

Objective:Viral resistance occurs with a high frequency after single-dose nevirapine. We aimed to evaluate the tolerance and resistance profiles of a combination of tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) given to HIV-1-infected delivering women and their newborns. Design:An open-label phase I/II trial in Cambodia, Côte d'Ivoire and South Africa. Methods:HIV-1-infected pregnant women received zidovudine from the enrollment until the beginning of labor, when single-dose nevirapine and two tablets of TDF/FTC were given. One daily tablet of TDF/FTC was then administered for 7 days postpartum. All infants received single-dose nevirapine with single-dose TDF (13 mg/kg) and single-dose FTC (2 mg/kg) and 1 week of zidovudine. Mothers and infants were followed for 2 months. Serious adverse events, kinetic of maternal plasma HIV-1 RNA, pediatric HIV infection and genotypic resistance and viral subtype were assessed. Results:Thirty-six HIV-1-infected pregnant women were enrolled: median age 28 years (interquartile range: 26–31 years), median CD4 cell count 462 cells/μl (interquartile range: 376–632) and median HIV-1 RNA 3.7 log10 copies/ml (interquartile range: 2.95–4.11). Two infants had clinical serious adverse events, including one who died (neonatal sepsis). One transient grade 3 neutropenia and two grade 3/4 hyperbilirubinemia were also reported in neonates. One HIV pediatric in-utero infection was diagnosed (2.8%; 95% confidence interval 0–15.4%). Genotypic viral resistance to nevirapine was detected in one mother out of 34 (2.9%) at one month postpartum, but was also detectable at enrollment. Conclusion:The combination of TDF/FTC to delivering women and their neonates appears well tolerated and to minimize the occurrence of nevirapine viral resistance.
Runge-Kutta-Based Explicit Local Time-Stepping Methods for Wave Propagation

Locally refined meshes severely impede the efficiency of explicit Runge--Kutta (RK) methods for the simulation of time-dependent wave phenomena. By taking smaller time-steps precisely where the smallest elements are located, local time-stepping (LTS) methods overcome the bottleneck caused by the stringent stability constraint of but a few small elements in the mesh. Starting from classical or low-storage explicit RK methods, explicit LTS methods of arbitrarily high accuracy are derived. When combined with an essentially diagonal finite element mass matrix, the resulting time-marching schemes retain the high accuracy, stability, and efficiency of the original RK methods while circumventing the geometry-induced stiffness. Numerical experiments with continuous and discontinuous Galerkin finite element discretizations corroborate the expected rates of convergence and illustrate the usefulness of these LTS-RK methods.
Analyzing User Password Selection Behavior for Reduction of Password Space

This paper presents a comprehensive survey of recent literature on the topic of password dictionaries for alphanumeric and graphical user authentication approaches including some password schemes proposed by the author. After different methods used for reduction of password space are introduced, they are analyzed and compared with the intent of finding a common flaw of user authentication mechanisms, which allows for the development of such password dictionaries by hackers. Our conclusion is that any user authentication system, which allows users to exercise choice in selection of their passwords, is vulnerable to the password space reduction methods presented in this paper and so should not be utilized
Extract of Artemisia lavandulaefolia Inhibits In Vitro Angiogenesis in Human Umbilical Vein Endothelial Cells

Angiogenesis is important processes for tumor growth and metastasis. Anti-angiogenesis target therapy has recently been known to be new anti-cancer therapeutic strategies. Natural products such as traditional medicine comprise a major source of angiogenesis inhibitors. Artemisia lavandulaefolia has been known to use in the traditional medical practices. However, its molecular mechanism on the tumor protection and therapy was not clearly elucidated. In this study, we investigated the possibility that extract of A. lavandulaefolia inhibits in vitro angiogenesis. Therefore, we examined the effect of extract of A. lavandulaefolia on the vascular network formation of human umbilical vein endothelial cells (HUVECs). We found that the treatment of A. lavandulaefolia extract suppressed the tube formation of HUVECs without any influence on the viability of HUVECs. In addition, extract of A. lavandulaefolia inhibited the migration and invasion of HUVECs. These results suggest that extract of A. lavandulaefolia could be act for an angiogenic inhibitor.