Miracle-dz/UniFAR-FTUs huggingface dataset:
The malaria merozoite, forty years on

SUMMARY The invasive blood stage of malaria parasites, merozoites, are complex entities specialized for the capture and entry of red blood cells. Their potential for vaccination and other anti-malaria strategies have attracted much research attention over the last 40 years, and there is now a considerable body of data relating to their biology. In this article some of the major advances over this period and remaining challenges are reviewed.
RecA4142 Causes SOS Constitutive Expression by Loading onto Reversed Replication Forks in Escherichia coli K-12

ABSTRACT Escherichia coli initiates the SOS response when single-stranded DNA (ssDNA) produced by DNA damage is bound by RecA and forms a RecA-DNA filament. recA SOS constitutive [recA(Con)] mutants induce the SOS response in the absence of DNA damage. It has been proposed that recA(Con) mutants bind to ssDNA at replication forks, although the specific mechanism is unknown. Previously, it had been shown that recA4142(F217Y), a novel recA(Con) mutant, was dependent on RecBCD for its high SOS constitutive [SOS(Con)] expression. This was presumably because RecA4142 was loaded at a double-strand end (DSE) of DNA. Herein, it is shown that recA4142 SOS(Con) expression is additionally dependent on ruvAB (replication fork reversal [RFR] activity only) and recJ (5′→3′ exonuclease), xonA (3′→5′ exonuclease) and partially dependent on recQ (helicase). Lastly, sbcCD mutations (Mre11/Rad50 homolog) in recA4142 strains caused full SOS(Con) expression in an ruvAB-, recBCD-, recJ-, and xonA-independent manner. It is hypothesized that RuvAB catalyzes RFR, RecJ and XonA blunt the DSE (created by the RFR), and then RecBCD loads RecA4142 onto this end to produce SOS(Con) expression. In sbcCD mutants, RecA4142 can bind other DNA substrates by itself that are normally degraded by the SbcCD nuclease.
Iranian Journal of Neurology © 2014 Original Paper a Comparison of Risk Factors and Severity of Ischemic Stroke in Female and Male Genders in North-west Iran: a Cross-sectional Study

Background: Gender difference has been reported in stroke risk factors and disease history. The aim of this study was to compare risk factors and the severity of ischemic stroke based upon modified Rankin Scale (mRS) and hospital mortality between two genders. Methods: In a cross-sectional study, 341 patients (44% males and 56% females with a mean age of 68.94 ± 12.74 years) with ischemic stroke, who were hospitalized in the neurology wards of two referral university hospital of NorthWest Iran (Imam Reza and Razi Hospitals), from the beginning to the end of 2011 were selected and assessed. Gender difference in terms of demographic findings, vascular risk factors, 7 th day mRS, and hospital mortality (during admission) were evaluated. Results: In 2.6% of cases, mRS was found to be less than 2 (favorable) and in 97.4% of cases; mRS was 2-5 (with disability). No significant difference in ischemic stroke severity based on mRS was observed between two genders. There was a significant difference in the rate of hypertension significant difference was seen in other risk factors between two genders. There was no significant difference in the mortality rate, which constituted 8.9% and 4.7% in females and males respectively (P = 0.140). Conclusion: The evidence from the present study suggests that despite the existence of some difference between risk-factors in two genders, there was no difference in terms of ischemic stroke severity and mortality rate between two genders.
Lung cancer and diesel exhaust: an updated critical review of the occupational epidemiology literature

A recent review concluded that the evidence from epidemiology studies was indeterminate and that additional studies were required to support the diesel exhaust-lung cancer hypothesis. This updated review includes seven recent studies. Two population-based studies concluded that significant exposure-response (E-R) trends between cumulative diesel exhaust and lung cancer were unlikely to be entirely explained by bias or confounding. Those studies have quality data on life-style risk factors, but do not allow definitive conclusions because of inconsistent E-R trends, qualitative exposure estimates and exposure misclassification (insufficient latency based on job title), and selection bias from low participation rates. Non-definitive results are consistent with the larger body of population studies. An NCI/NIOSH cohort mortality and nested case-control study of non-metal miners have some surrogate-based quantitative diesel exposure estimates (including highest exposure measured as respirable elemental carbon (REC) in the workplace) and smoking histories. The authors concluded that diesel exhaust may cause lung cancer. Nonetheless, the results are non-definitive because the conclusions are based on E-R patterns where high exposures were deleted to achieve significant results, where a posteriori adjustments were made to augment results, and where inappropriate adjustments were made for the “negative confounding” effects of smoking even though current smoking was not associated with diesel exposure and therefore could not be a confounder. Three cohort studies of bus drivers and truck drivers are in effect air pollution studies without estimates of diesel exhaust exposure and so are not sufficient for assessing the lung cancer-diesel exhaust hypothesis. Results from all occupational cohort studies with quantitative estimates of exposure have limitations, including weak and inconsistent E-R associations that could be explained by bias, confounding or chance, exposure misclassification, and often inadequate latency. In sum, the weight of evidence is considered inadequate to confirm the diesel-lung cancer hypothesis.
Plasma folate levels and risk of spontaneous abortion.

CONTEXT Both folate deficiency and folic acid supplements have been reported to increase the risk of spontaneous abortion. The results are inconclusive, however, and measurements of folate have not been available in all studies. OBJECTIVE To study the association between plasma folate levels and the risk of spontaneous abortion. DESIGN, SETTING, AND POPULATION Population-based, matched, case-control study of case women with spontaneous abortion and control women from January 1996 through December 1998 in Uppsala County, Sweden. Plasma folate measurements were available for 468 cases and 921 controls at 6 to 12 gestational weeks. MAIN OUTCOME MEASURE Risk of spontaneous abortion vs maternal plasma folate level. RESULTS Compared with women with plasma folate levels between 2.20 and 3.95 ng/mL (5.0 and 8.9 nmol/L), women with low (< or =2.19 ng/mL [< or =4.9 nmol/L]) folate levels were at increased risk of spontaneous abortion (adjusted odds ratio [OR], 1.47; 95% confidence interval [CI], 1.01-2.14), whereas women with higher folate levels (3.96-6.16 ng/mL [9.0-13.9 nmol/L] and > or =6.17 ng/mL [> or =14.0 nmol/L]) showed no increased risk of spontaneous abortion (OR, 0.84; 95% CI, 0.59-1.20; and OR, 0.74; 95% CI, 0.47-1.16, respectively). Low folate levels were associated with a significantly increased risk when the fetal karyotype was abnormal (OR, 1.95; 95% CI, 1.09-3.48) but not when the fetal karyotype was normal (OR, 1.11; 95% CI, 0.55-2.24) or unknown (OR, 1.45; 95% CI, 0.90-2.33). CONCLUSION Low plasma folate levels were associated with an increased risk of early spontaneous abortion.
IC implementation of spike-timing-dependent synaptic plasticity model using low capacitance value

A number of recent studies on neural networks have been conducted with the purpose of applying engineering to the brain. An artificial neural networks (ANNs) were created that focus on how learning is achieved. In this paper, we focus on spike-timing-dependent synaptic plasticity (STDP) and construct an STDP model using semiconductors. We propose a new STDP model using a low capacitance value with CMOS technology, and show that the proposed integrated circuit has similar characteristics to biological neural networks.
Overview of resilience mechanisms based on multipath structures

Multipath structures are the base for many recently developed rerouting and protection switching mechanisms. All of these methods show a similar path layout, rely on traffic distribution, and promise resilience with only little backup capacity. Therefore, it is hard to recognize their commonalities and differences at first sight. This paper provides an overview of these related mechanisms and a comparative analysis regarding their applicability in optical and packet switched technologies, their path layout, their reaction time, their dynamic adaptability, and many other aspects.
Complications preceding early deaths in Black and White children with acute myeloid leukemia

Black patients have a twofold increased risk of induction mortality compared to White patients with acute myeloid leukemia (AML). We reviewed diagnosis and billing data from Pediatric Health Information System for 28 AML Induction I deaths to investigate conditions preceding death in White and Black patients. Half of deaths occurred within 10 days of initial diagnostic admission. Respiratory, cardiac, renal, and infectious complications were common prior to both White and Black deaths. Deaths in White patients were more commonly preceded by intracranial hemorrhage compared to deaths in Black patients. Future studies should assess management approaches of complications by race to identify modifiable processes that reduce mortality.
Face Recognition, Neurophysiology, and Neural Technology

The recognition of other individuals is a major prerequisite for human social interaction and hence a rather important brain function. The most prominent cue for that recognition is the face. The capability to recognize persons from their faces is part of a spectrum of related skills, which include face segmentation, i.e., finding faces in a scene or image, the estimation of the pose, the direction of gaze, and the person’s emotional state. This article focuses on recognition of identity, a more detailed treatment of the other aspects can be found in [Face Recognition, Psychology, and Connectionism].
The Max $K$-Armed Bandit: PAC Lower Bounds and Efficient Algorithms

We consider the Max $K$-Armed Bandit problem, where a learning agent is faced with several stochastic arms, each a source of i.i. d. rewards of unknown distribution. At each time step the agent chooses an arm, and observes the reward of the obtained sample. Each sample is considered here as a separate item with the reward designating its value, and the goal is to find an item with the highest possible value. Our basic assumption is a known lower bound on the {\em tail function} of the reward distributions. Under the PAC framework, we provide a lower bound on the sample complexity of any $(\epsilon,\delta)$-correct algorithm, and propose an algorithm that attains this bound up to logarithmic factors. We analyze the robustness of the proposed algorithm and in addition, we compare the performance of this algorithm to the variant in which the arms are not distinguishable by the agent and are chosen randomly at each stage. Interestingly, when the maximal rewards of the arms happen to be similar, the latter approach may provide better performance.
Arp2/3 complex is bound and activated by two WASP proteins

Actin related protein 2/actin related protein 3 (Arp2/3) complex nucleates new actin filaments in eukaryotic cells in response to signals from proteins in the Wiskott–Aldrich syndrome protein (WASP) family. The conserved VCA domain of WASP proteins activates Arp2/3 complex by inducing conformational changes and delivering the first actin monomer of the daughter filament. Previous models of activation have invoked a single VCA acting at a single site on Arp2/3 complex. Here we show that activation most likely involves engagement of two distinct sites on Arp2/3 complex by two VCA molecules, each delivering an actin monomer. One site is on Arp3 and the second is on ARPC1 and Arp2. The VCAs at these sites have distinct roles in activation. Our findings reconcile apparently conflicting literature on VCA activation of Arp2/3 complex and lead to a new model for this process.
Anatomic Considerations for Plate‐Screw Fixation of the Cervical Spine

A cadaveric study was done to investigate the variability of interfacet distances from C3 to C7, to learn pedicle morphology at C7-T2, and to determine potential dangers of plate-screw osteosynthesis technique of the cervical spine. Twenty-two cadavers were dissected from C2 to C7 to expose the lateral masses and nerve roots. The interfacet distances from the center of the lateral mass to the next lateral mass from C3 to C7 vary widely among different individuals, ranging from 9 mm to 16 (average, 13 mm). A new plate design is necessary to better accommodate the differences in interfacet distances among different patients and different levels. The second part of the study involved 11 dissected cadaveric specimens of the cervicothoracic junction. The pedicle entry point was 1 mm inferior to the midportion of the facet joint for C7, T1, and T2. The medial angulation averaged 34° at C7, 31.8° at T1, and 26.5° at T2. The mediolateral and superoinferior outer pedicle diameters were 6.9 mm and 7.5 mm at C7, 8.5 mm and 9.5 mm at T1, and 7.5 mm and 10.7 mm at T2, respectively. The mediolateral inner diameter averaged 5.18 mm, 6.4 mm, 5.5 mm for C7, T1 and T2, respectively. The pedicle distances (from the entry point to the posterior vertebral body line) measured 9.1 mm, 9.9 mm, and 10.4 mm for respective levels. The margins for error are small when using pedicle screws at these levels. If a pedicle screw must be used at C7, T1, and T2, one must have precise knowledge of the entrance point, diameters, and 25–30° medial direction. The third part of the experiment involved 18 fresh cadaveric specimens for the study of the anatomy of the nerve root, vertebral artery, and spinal cord in relation to drill trajectory and inserted screws. The vertebral artery and spinal cord were virtually free of danger with known techniques. The purpose of this experiment was then to find the trajectory that is safest for the nerve roots. The nerve root exits at the anterolateral portion of the superior facet, and the more medial angulation or the more cephalad angulation of the screw, the more likely it is to impinge on the nerve root. The ideal exit point of the drill was determined to be the juncture between the transverse process and the facet. The safest screw direction is determined to be 33° lateral and 17° cephalad starting 1 mm medial to the center of the lateral mass for C3-C6 in order to avoid both the nerve root and the facet joint. The depth of these screws ranged from 7 mm to 18 mm with an average of 10 mm, using this technique. The lateral mass is thin at the transitional C7 level, and lateral mass screw is dangerous in disrupting the nerve root or the facet joint.
CUSA and CUDE: GPU-Accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation

It is well-established that a linear correlation exists between accessible surface areas and experimentally measured solvation energies. Combining this knowledge with an analytic formula for calculation of solvent accessible surfaces, we derive a simple model of desolvation energy as a differentiable function of atomic positions. Additionally, we find that this algorithm is particularly well suited for hardware acceleration on graphics processing units (GPUs), outperforming the CPU by up to two orders of magnitude. We explore the scaling of this desolvation algorithm and provide implementation details applicable to general pairwise algorithms.
A New Structure for Nonisolated Boost DC-DC Converter

In this paper, a new structure of nonisolated boost DC–DC converters is proposed. The operation of the proposed structure in continuous conduction mode (CCM) and discontinuous conduction mode (DCM) is presented. Then, the critical inductance relation between CCM and DCM is obtained. The voltage gain and current stress of switches are calculated. Finally, the validity of the presented theoretical issues is reconfirmed by using simulation results obtained from PSCAD/EMTDC software.
Indium Nitride and Indium Gallium Nitride layers grown on nanorods

Molecular beam epitaxy has been used to grow InN layers on both Si and SiC substrates and In0.5Ga0. 5N layers on Si substrates using a nanorod precursor array. Transmission electron microscopy (TEM) studies show that nanorods grown first under N-rich conditions, and then under more metal-rich conditions to promote lateral growth are free of dislocations until coalescence occurs. At coalescence, dislocations are introduced at grain boundaries. These are predominantly twist boundaries, with better epitaxial alignment seen on SiC substrates. The lateral growth of In0.5Ga0. 5N is shown to be cubic, tentatively ascribed to the growth of basal plane stacking faults at the start of the lateral growth and the low growth temperatures used.
The orientation specificity of two visual after‐effects

1. Inspection of a high‐contrast adapting grating produces two visual after‐effects: (a) the contrast threshold is raised for test gratings of similar spatial frequency to that of the adapting pattern and (b) the apparent spatial frequency of test gratings shifts away from that of the adapting grating—higher frequencies seem higher and lower ones lower than they really are.
Image-Based Localization Using Hourglass Networks

In this paper, we propose an encoder-decoder convolutional neural network (CNN) architecture for estimating camera pose (orientation and location) from a single RGB-image. The architecture has a hourglass shape consisting of a chain of convolution and up-convolution layers followed by a regression part. The up-convolution layers are introduced to preserve the fine-grained information of the input image. Following the common practice, we train our model in end-to-end manner utilizing transfer learning from large scale classification data. The experiments demonstrate the performance of the approach on data exhibiting different lighting conditions, reflections, and motion blur The results indicate a clear improvement over the previous state-of-the-art even when compared to methods that utilize sequence of test frames instead of a single frame.
A Simulation-Based Scalability Study of Parallel Systems

Scalability studies of parallel architectures have used scalar metrics to evaluate their performance. Very often, it is difficult to glean the sources of inefficiency resulting from the mismatch between the algorithmic and architectural requirements using such scalar metrics. Low-level performance studies of the hardware are also inadequate for predicting the scalability of the machine on real applications. We propose a top-down approach to scalability study that alleviates some of these problems. We characterize applications in terms of the frequently occurring kernels, and their interaction with the architecture in terms of overheads in the parallel system. An overhead function is associated with each artifact of the parallel system that limits its scalability. We present a simulation platform called SPASM (Simulator for Parallel Architectural Scalability Measurements) that quantifies these overhead functions. SPASM separates the algorithmic overhead into its components (such as serial and work-imbalance overheads), and interaction overhead into its components (such as latency and contention). Such a separation is novel and has not been addressed in any previous study using real applications. We illustrate the top-down approach by considering a case study in implementing three NAS parallel kernels on two simulated message-passing platforms.
ITL-MINE: Mining Frequent Itemsets More Efficiently

The discovery of association rules is an important problem in data mining. It is a two-step process consisting of finding the frequent itemsets and generating association rules from them. Most of the research attention is focused on efficient methods of finding frequent itemsets because it is computationally the most expensive step. In this paper, we present a new data structure and a more efficient algorithm for mining frequent itemsets from typical data sets. The improvement is achieved by scanning the database just once and by reducing item traversals within transactions. We present performance comparisons of our algorithm against the fastest Apriori implementation and the recently developed H-Mine algorithm. These results show that our algorithm outperforms both Apriori and HMine on several widely used test data sets.
Study of an Infant with a Gastric Fistula and Her Normal Twin

&NA; A set of identical twins, one of whom had congenital esophageal stenosis, was studied in an attempt to gain further understanding of the relationship between the subjects' affect, object relations, the perception of food, and motor activity on the one hand, and the stomach's secretion of hydrochloric acid on the other. Increased secretory rates were associated with the outgoing affects, especially in the presence of the mother. Variable rates were associated with activity and certain object relationships, and decreased rates of secretion were associated with depression and with a separation from the mother. The findings contribute to our knowledge of the physiological correlates of the oral phase of psychosexual development.
Curcumin Chemosensitizes 5-Fluorouracil Resistant MMR-Deficient Human Colon Cancer Cells in High Density Cultures

Objective Treatment of colorectal cancer (CRC) remains a clinical challenge, as more than 15% of patients are resistant to 5-Fluorouracil (5-FU)-based chemotherapeutic regimens, and tumor recurrence rates can be as high as 50–60%. Cancer stem cells (CSC) are capable of surviving conventional chemotherapies that permits regeneration of original tumors. Therefore, we investigated the effectiveness of 5-FU and plant polyphenol (curcumin) in context of DNA mismatch repair (MMR) status and CSC activity in 3D cultures of CRC cells. Methods High density 3D cultures of CRC cell lines HCT116, HCT116+ch3 (complemented with chromosome 3) and their corresponding isogenic 5-FU-chemo-resistant derivative clones (HCT116R, HCT116+ch3R) were treated with 5-FU either without or with curcumin in time- and dose-dependent assays. Results Pre-treatment with curcumin significantly enhanced the effect of 5-FU on HCT116R and HCR116+ch3R cells, in contrast to 5-FU alone as evidenced by increased disintegration of colonospheres, enhanced apoptosis and by inhibiting their growth. Curcumin and/or 5-FU strongly affected MMR-deficient CRC cells in high density cultures, however MMR-proficient CRC cells were more sensitive. These effects of curcumin in enhancing chemosensitivity to 5-FU were further supported by its ability to effectively suppress CSC pools as evidenced by decreased number of CSC marker positive cells, highlighting the suitability of this 3D culture model for evaluating CSC marker expression in a close to vivo setting. Conclusion Our results illustrate novel and previously unrecognized effects of curcumin in enhancing chemosensitization to 5-FU-based chemotherapy on DNA MMR-deficient and their chemo-resistant counterparts by targeting the CSC sub-population. (246 words in abstract).