Miracle-dz/UniFAR-FTUs huggingface dataset:
Inter- and intraspecies identification of Bartonella (Rochalimaea) species

Species of the genus Rochalimaea, recently renamed Bartonella, are of a growing medical interest. Bartonella quintana was reported as the cause of trench fever, endocarditis, and bacillary angiomatosis. B. henselae has been implicated in symptoms and infections of human immunodeficiency virus-infected patients, such as fever, endocarditis, and bacillary angiomatosis, and is involved in the etiology of cat scratch disease. Such a wide spectrum of infections makes it necessary to obtain an intraspecies identification tool in order to perform epidemiological studies. B. vinsonii, B. elizabethae, seven isolates of B. quintana, and four isolates of B. henselae were studied by pulsed-field gel electrophoresis (PFGE) after restriction with the infrequently cutting endonucleases NotI, EagI, and SmaI. Specific profiles were obtained for each of the four Bartonella species. Comparison of genomic fingerprints of isolates of the same species showed polymorphism in DNA restriction patterns, and a specific profile was obtained for each isolate. A phylogenetic analysis of the B. quintana isolates was obtained by using the Dice coefficient, UPGMA (unweighted pair-group method of arithmetic averages), and Package Philip programming. Amplification by PCR and subsequent sequencing using an automated laser fluorescent DNA sequencer (Pharmacia) was performed on the intergenic spacer region (ITS) between the 16 and 23S rRNA genes. It was found that each B. henselae isolate had a specific sequence, while the B. quintana isolates fell into only two groups. When endonuclease restriction analysis of the ITS PCR product was done, three enzymes, TaqI, HindIII, and HaeIII, allowed species identification of Bartonella spp. Restriction fragment length polymorphism after PCR amplification of the 16S-23S rRNA gene ITS may be useful for rapid species identification, and PFGE could be an efficient method for isolate identification.
Online Appendix: Preferences for Flexibility and Randomization under Uncertainty

In this online appendix, we present an extension of Theorem 1. We show that an RUA representation can incorporate the variational preferences of Maccheroni, Marinacci, and Rustichini (2006), which are general enough to incorporate other well-known uncertainty-averse preferences, such as the maxmin preferences of Gilboa and Schmeidler (1989), the multiplier preferences of Hansen and Sargent (2001), and the vector-expected utility preferences of Siniscalchi (2009). We present the extension of Theorem 1 in Section 1. The proof is in Section 2. In Section 3, we provide the omitted proofs of Lemmas 1 and 2 in the proof of Theorem 1.
Watchdog: Hardware for safe and secure manual memory management and full memory safety

Languages such as C and C++ use unsafe manual memory management, allowing simple bugs (i.e., accesses to an object after deallocation) to become the root cause of exploitable security vulnerabilities. This paper proposes Watchdog, a hardware-based approach for ensuring safe and secure manual memory management. Inspired by prior software-only proposals, Watchdog generates a unique identifier for each memory allocation, associates these identifiers with pointers, and checks to ensure that the identifier is still valid on every memory access. This use of identifiers and checks enables Watchdog to detect errors even in the presence of reallocations. Watchdog stores these pointer identifiers in a disjoint shadow space to provide comprehensive protection and ensure compatibility with existing code. To streamline the implementation and reduce runtime overhead: Watchdog (1) uses micro-ops to access metadata and perform checks, (2) eliminates metadata copies among registers via modified register renaming, and (3) uses a dedicated metadata cache to reduce checking overhead. Furthermore, this paper extends Watchdog's mechanisms to detect bounds errors, thereby providing full hardware-enforced memory safety at low overheads.
Update in diffuse parenchymal lung disease 2010.

In 2010, important articles have been published in the field of diffuse parenchymal lung diseases (DPLD). Many of those deal with idiopathic pulmonary fibrosis (IPF), which is the most aggressive form of DPLD (1). With pirfenidone, the first drug has been approved for the specific treatment of IPF in the European Union. However, the FDA refused to approve pirfenidone for the U.S. market. We summarize articles from this and other journals that have provided important new findings in the field of DPLD, with a particular focus on the clinical and experimental advances in IPF.
Asymmetrical, agonist‐induced fluctuations in local extracellular [Ca2+] in intact polarized epithelia

We recently proposed that extracellular Ca2+ ions participate in a novel form of intercellular communication involving the extracellular Ca2+‐sensing receptor (CaR). Here, using Ca2+‐selective microelectrodes, we directly measured the profile of agonist‐induced [Ca2+]ext changes in restricted domains near the basolateral or luminal membranes of polarized gastric acid‐secreting cells. The Ca2+‐mobilizing agonist carbachol elicited a transient, La3+‐sensitive decrease in basolateral [Ca2+] (average ≈250 μM, but as large as 530 μM). Conversely, carbachol evoked an HgCl2‐sensitive increase in [Ca2+] (average ≈400 μM, but as large as 520 μM) in the lumen of single gastric glands. Both responses were significantly reduced by pre‐treatment with sarco‐endoplasmic reticulum Ca2+ ATPase (SERCA) pump inhibitors or with the intracellular Ca2+ chelator BAPTA‐AM. Immunofluores cence experiments demonstrated an asymmetric localization of plasma membrane Ca2+ ATPase (PMCA), which appeared to be partially co‐localized with CaR and the gastric H+/K+‐ATPase in the apical membrane of the acid‐secreting cells. Our data indicate that agonist stimulation results in local fluctuations in [Ca2+]ext that would be sufficient to modulate the activity of the CaR on neighboring cells.
A new scheme to improve the secrecy throughput under the constraints of secrecy outage probability and average transmit power

The issue of physical layer security for the wireless communication with slow fading is addressed in this paper, and the secrecy outage performance is concerned. The system is modeled as a wiretap channel, and each of the transmitter and receivers is equipped with a single antenna. The channel state information (CSI) about the channel from the transmitter to the legitimate receiver (the main channel) is assumed to be perfectly known by the transmitter and the receivers, while the transmitter does not know the CSI about the channel from the transmitter to the eavesdropper (the eavesdropper's channel) but its probability density function (PDF). Differing from the fixed secrecy rate scheme and the on/off scheme in the literature, this paper adaptively chooses the secrecy rate. The secrecy rate for each value of the main channel gain is determined by the required secrecy outage probability and the PDF of the eavesdropper's channel, and the secrecy throughput is maximized under the constraint of the transmit power for the required secrecy outage probability. The quasi-static Rayleigh fading channel is used to compare our scheme with the two existing schemes, and simulation results show that our scheme outperforms them when small secrecy outage probabilities are required.
Physiologic monitoring.

This chapter will provide a review of modern concepts of cardiovascular monitoring with emphasis on essential hemodynamic variables in the early post cardiac surgery patient. When defining circulatory function, importance of the entire circulatory system is underscored. This includes the function and interaction of the heart, blood vessels and circulatory blood volume to deliver sufficient amount of oxygenated blood to tissue beds. In post cardiac surgery patients, the pulmonary artery catheter remains the most widely used technology to assess cardiac function. This chapter highlights the importance of validation of less invasive and noninvasive hemodynamic monitors for the management of critically ill patients and early post cardiac surgery patients. In addition, this chapter describes the evolution of monitoring of post cardiac surgery and critically ill patients, examines different monitoring technologies and address controversial questions in modern practice as well as future directions.
Enhanced Classification of Brugada Syndrome–Associated and Long-QT Syndrome–Associated Genetic Variants in the SCN5A-Encoded Nav1.5 Cardiac Sodium Channel

Background—A 2% to 5% background rate of rare SCN5A nonsynonymous single nucleotide variants (nsSNVs) among healthy individuals confounds clinical genetic testing. Therefore, the purpose of this study was to enhance interpretation of SCN5A nsSNVs for clinical genetic testing using estimated predictive values derived from protein-topology and 7 in silico tools. Methods and Results—Seven in silico tools were used to assign pathogenic/benign status to nsSNVs from 2888 long-QT syndrome cases, 2111 Brugada syndrome cases, and 8975 controls. Estimated predictive values were determined for each tool across the entire SCN5A-encoded Nav1.5 channel as well as for specific topographical regions. In addition, the in silico tools were assessed for their ability to correlate with cellular electrophysiology studies. In long-QT syndrome, transmembrane segments S3–S5+S6 and the DIII/DIV linker region were associated with high probability of pathogenicity. For Brugada syndrome, only the transmembrane spanning domains had a high probability of pathogenicity. Although individual tools distinguished case- and control-derived SCN5A nsSNVs, the composite use of multiple tools resulted in the greatest enhancement of interpretation. The use of the composite score allowed for enhanced interpretation for nsSNVs outside of the topological regions that intrinsically had a high probability of pathogenicity, as well as within the transmembrane spanning domains for Brugada syndrome nsSNVs. Conclusions—We have used a large case/control study to identify regions of Nav1.5 associated with a high probability of pathogenicity. Although topology alone would leave the variants outside these identified regions in genetic purgatory, the synergistic use of multiple in silico tools may help promote or demote a variant’s pathogenic status.
The sum of digits of primes inZ(i)

We study the distribution of the complex sum-of-digits function sq with basis q = ia § i, a 2 Z + for Gaussian primes p. Inspired by a recent result of Mauduit and Rivat [16] for the real sum-of-digits function, we here get uniform distribution modulo 1 of the sequence (fisq(p)) provided fi 2R nQ and q is prime with a ‚ 28. We also determine the order of magnitude of the number of Gaussian primes whose sum-of-digits evaluation lies in some fixed residue class mod m.
Prediction of adverse pregnancy outcome by the presence of lupus anticoagulant, but not anticardiolipin antibody, in patients with antiphospholipid antibodies.

OBJECTIVE To investigate which serologic and clinical findings predict adverse pregnancy outcome in patients with antiphospholipid antibody (aPL) and to test the hypothesis that a pattern of clinical and serologic variables can identify women at highest risk of adverse pregnancy outcome. METHODS Women enrolled in a multicenter prospective observational study of risk factors for adverse pregnancy outcome in patients with aPL (lupus anticoagulant [LAC], anticardiolipin antibody [aCL], and/or antibody to β2-glycoprotein I [anti-β2 GPI]) and/or systemic lupus erythematosus (SLE) were recruited for the present prospective study. Demographic, clinical, serologic, and treatment data were recorded at the time of the first study visit. The relationship between individual and combined variables and adverse pregnancy outcome was assessed by bivariate and multivariate analysis. RESULTS Between 2003 and 2011 we enrolled 144 pregnant patients, of whom 28 had adverse pregnancy outcome. Thirty-nine percent of the patients with LAC had adverse pregnancy outcome, compared to 3% of those who did not have LAC (P<0.0001). Among women with IgG aCL at a level of ≥40 units/ml, only 8% of those who were LAC negative had adverse pregnancy outcome, compared to 43% of those who were LAC positive (P=0.002). IgM aCL, IgG anti-β2 GPI, and IgM anti-β2 GPI did not predict adverse pregnancy outcome. In bivariate analysis, adverse pregnancy outcome occurred in 52% of patients with and 13% of patients without prior thrombosis (P=0.00005), and in 23% with SLE versus 17% without SLE (not significant); SLE was a predictor in multivariate analysis. Prior pregnancy loss did not predict adverse pregnancy outcome. Simultaneous positivity for aCL, anti-β2 GPI, and LAC did not predict adverse pregnancy outcome better than did positivity for LAC alone. CONCLUSION LAC is the primary predictor of adverse pregnancy outcome after 12 weeks' gestation in aPL-associated pregnancies. Anticardiolipin antibody and anti-β2 GPI, if LAC is not also present, do not predict adverse pregnancy outcome.
3-D Rehabilitation Robot System for Upper Limbs and its Force Display Techniques

Movements of upper limbs are complicated, various and indispensable for daily activities. For patients with impairment of their upper limb, rehabilitation along with medical treatment is needed to recover function. For elderly as well, training is needed to keep their ADL or social activities. Application of robotics and virtual reality technology makes possible for new training methods and exercises and for quantitative evaluations to enhance the qualitative effect of training. However it is difficult for conventional robots to be commercialized for rehabilitation use because of safety insufficiency. The authors have involved in a project managed by NEDO (New Energy and Industrial Technology Development Organization), “Rehabilitation System for the Upper Limbs and Lower Limbs,” and developed a 3-DOF exercise machine for upper limb (EMUL). In this paper, the authors report on EMUL which has been developed considering safety. They also mention some software with force display by EMUL, which can help doctors and therapists with their treatment.
Evolution of Dengue Disease and Entomological Monitoring in Santa Cruz, Bolivia 2002 – 2008

Background In the context of a rapid increase of dengue cases in the Americas, a monitoring system based on systematic serological control (IgM) of patients consulting for suspected dengue was developed in Bolivia at the end of the 1990s. In the most affected city of Santa Cruz, this system was complemented by an entomological surveillance program based on periodical search for immature stages of Aedes aegypti in dwelling water-holding containers. Here, we analyze these data and describe dengue patterns over 6 years (2002–2008), highlighting the spatial distribution of patients and vectors. Methodology /Principal Findings Data mining concerned six annual epidemic cycles (2002–2008), with continuous serological and clinical results and entomological data from 16 surveys, examined at the scales of 36 urban areas and four concentric areas covering the entire city. Annual incidence varied from 0.28‰ to 0.95‰; overall incidence was higher in women and adults, and dengue dynamics followed successive periods of high (January–June) and low (July–December) transmission. Lower numbers of cases from the city center to the periphery were observed, poorly related to the more homogeneous and permanent distribution of A. aegypti. "Plant pots" were a major vector source in the city center, and "Tires" and "Odds and ends" beyond the second ring of the city. Conclusions/Significance Over the years, the increasing trend of dengue cases has been highlighted as well as its widespread distribution over the entire city, but an underestimation of the number of cases is strongly suspected. Contrary to popular belief, the city center appears more affected than the periphery, and dengue is not particularly related to waste. Interestingly, the clinical diagnosis of dengue by physicians improved over the years, whatever the gender, age and residential area of suspected cases.
Gastric motility function in critically ill patients tolerant vs intolerant to gastric nutrition.

BACKGROUND Administration of gastric enteral nutrition (EN) in the intensive care unit (ICU) is commonly impeded by high gastric residual volumes (GRV). This study evaluated gastric emptying in patients with limited GRV (tolerant group) vs volumes > or =150 mL (intolerant group) and whether prokinetic therapy improves gastric motility in intolerant patients. METHODS To assess gastric motility, mechanically ventilated patients received acetaminophen 975 mg, and peak plasma concentration (Cmax), concentration at 60 minutes (C(60)), time to Cmax (Tmax), and area under the concentration-time curve from 0 to 60 minutes (AUC(0-60)) were determined. This evaluation was repeated in intolerant patients after 24 hours of either erythromycin 250 mg or metoclopramide 10 mg therapy, both administered intravenously every 6 hours. RESULTS Ten tolerant and 20 intolerant patients were studied. Tolerant patients had significantly greater Cmax (14.12 +/- 7.25 vs 9.28 +/- 5.22 mg/L; p < .05), C(60) (9.62 +/- 4.65 vs 6.08 +/- 4.00 mg/L; p < .001), and AUC(0-60) (10.01 +/- 5.97 vs 3.93 +/- 2.84 mg/h/L; p < .01) and shortened Tmax (0.81 +/- 0.61 vs 1.98 +/- 1.26 hours; p < .001) compared with intolerant patients. After prokinetic therapy, Cmax (15.26 +/- 8.85 mg/L), C(60) (11.96 +/- 5.99 mg/L), and AUC(0-60) (10.90 +/- 6.57 mg/h/L) increased and Tmax (1.07 +/- 1.01 hours) decreased in the intolerant group to values similar to the tolerant group. CONCLUSIONS ICU patients with elevated GRV during gastric EN have delayed gastric motility. Initiating prokinetic therapy accelerates gastric emptying to resemble that of ICU patients tolerating EN.
A New Parallel Paradigm for Block-Based Gauss-Jordan Algorithm

Two kinds of parallel possibilities which are intrastep and inter-steps parallelism exist in the block-based Gauss-Jordan algorithm which is a classical method of large scale matrix inversion. But the existing parallel paradigm of Block-based Gauss-Jordan algorithm just aiming at the intra-step parallelism, can’t meet the requirement of making more tasks executed simultaneously in high performance platform can be harnessed more and more computing resources. To overcome the problem described above, this paper presents a hybrid parallel paradigm exploiting all the possible parallelizable parts of the Gauss-Jordan algorithm. In this hybrid parallel paradigm, 1) Divide and conquer paradigm is responsible for decomposing the large granularity task into sub-tasks as much as possible; 2) Single program multi data (SPMD) paradigm deals with intra-step parallelism in the algorithm; 3) Data pipelining paradigm helps to solve the problem of inter-steps parallelism. Finally some experiments based on comparison the hybrid parallel paradigm with the existing parallel paradigm show us the good performance of our paradigm.
Identification of Target Messenger RNA Substrates for the Murine Deleted in Azoospermia-Like RNA-Binding Protein1

Abstract The murine autosomal deleted in azoospermia-like protein (mDAZL) is a germ cell-restricted RNA-binding protein essential for sperm production. Homozygous disruption of the mDAZL gene results in the absence of germ cells beyond the spermatogonial stage. Progress into the function of DAZL in spermatogenesis has been hampered without identification of the cognate mRNA substrates that it binds to and regulates. Using the isolation of specific nucleic acids associated with proteins (SNAAP) technique recently developed in our lab, we identified mRNAs from testis that were specifically bound by mDAZL. One mRNA encoded the Tpx-1 protein, a testicular cell adhesion protein essential for the progression of spermatogenesis. A 26-nucleotide region necessary and sufficient to bind mDAZL was found within additional mRNAs isolated by the screen. These included mRNA encoding Pam, a protein associated with myc; GRSF1, an mRNA-binding protein involved in translation activation, and TRF2, a TATA box-binding protein-like protein involved in transcriptional regulation. Each mRNA containing the mDAZL binding site was specifically bound by mDAZL. A similar sequence is also present in the Cdc25A mRNA, a threonine/tyrosine phosphatase involved in cell cycle progression. The mDAZL and Cdc25A homologues are functionally linked in Drosophila and are necessary for spermatogenesis. Our demonstration that Tpx-1 and Cdc25A mRNAs are bound by mDAZL suggests that mDAZL regulates a subset of mRNAs necessary for germ cell development and cell cycle progression. Understanding how mDAZL regulates the target mRNAs will provide new insights into spermatogenesis, strategies for therapeutic intervention in azoospermic patients, and novel approaches for male contraception.
Forced Convective Heat Transfer of Nanofluids in Minichannels

Nanofluids are a new class of heat transfer fluids which are engineered by dispersing nanometer-sized metallic or non-metallic solid particles or tubes in conventional heat transfer fluids such as water, ethylene glycol, and engine oil. This is a rapidly emerging interdisciplinary field where nanoscience, nanotechnology, and thermal engineering meet. Since this novel concept of nanofluids was innovated in the mid-last decade (Choi, 1995), this research topic has attracted tremendous interest from researchers worldwide due to their fascinating thermal characteristics and potential applications in numerous important fields such as microelectronics, transportation, and biomedical. With an ever-increasing thermal load due to smaller features of microelectronic devices and more power output, cooling for maintaining desirable performance and durability of such devices is one of the most important technical issues in many high-tech industries. Although increased heat transfer can be achieved creating turbulence, increasing heat transfer surface area and other way, the heat transfer performance will ultimately be limited due to the low thermal properties of these conventional fluids. If extended heating surface is used to obtain high heat transfer, it also undesirably increases the size of the thermal management system. Thus, these conventional cooling techniques are not suitable to meet the cooling demand of these high-tech industries. There was therefore a need for new and efficient heat transfer liquids that can meet the cooling challenges for advanced devices as well as energy conversion-based applications and the innovation of nanofluids has opened the door to meet those cooling challenges. In the field of heat transfer, all liquid coolants currently used at low and moderate temperatures exhibit very poor thermal conductivity and heat storage capacity resulting in their poor convective heat transfer performance. Although thermal conductivity of a fluid plays a vital role in the development of energy-efficient heat transfer equipments and other cooling technologies, the traditional heat transfer fluids possess orders-of-magnitude smaller thermal conductivity than metallic or nonmetallic particles. For example, thermal conductivities of water and engine oil are about 5000 times and 21000 times, respectively smaller than that of multi-walled carbon nanotubes (MWCNT) as shown in Table 1 which provides values of thermal conductivities of various commonly used liquids and nanoparticle materials at room temperature. Therefore, the thermal conductivities of fluids