Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of ultrasonic pretreatment on quantity and composition of bacterial DNA recovered from granular activated carbon used for drinking water treatment

Effects of ultrasonic pretreatment on bacterial DNA recovery from granular activated carbon (GAC) were investigated. GAC (Calgon F400), biologically activated, was sampled from an actual drinking water plant. Different ultrasonic energy densities (0–400 J·cm−3) were applied with agitation (250 rpm for 30 min), and recovered bacterial DNA was quantified using quantitative PCR. Energy density was linearly correlated with the concentration of carbon fines produced from GAC during ultrasonication. Ultrasonication alone had no effect on DNA recovery at ≤60 J·cm−3, but a strongly adverse effect at >67 J·cm−3 due to the produced carbon fines. Agitation along with ultrasonication strongly enhanced the bacterial DNA recovery when ≤40 J·cm−3 was applied, although it did not affect the production of carbon fines. Ribosomal tag pyrosequencing was used to compare recovered bacterial communities (0, 20 and 30 J·cm−3 with or without agitation). Ultrasonication allowed for obtaining a more diverse and richer bacterial community from GAC, compared with the control. Agitation did not show a positive effect on community organization (richness and diversity). Consistently, canonical correspondence analysis indicated that the energy density was associated with the relative abundances of particular bacterial members (P < 0.05), while agitation did not. Correspondence analysis revealed that the recovered bacterial communities were grouped according to the applied energy densities. In conclusion, ultrasonication and agitation influence the recovered DNA in quality and quantity, respectively, and carbon fines as a by-product by ultrasonication interfere with the DNA recovery.
Self -correction algorithms used in performance optimization of wireless battery charger

This paper focuses on wireless power transfer based on Witricity technology, specifically wireless battery charger application for electric vehicle. In order to reach efficient power transfer, a principle of coupling magnetic resonance at high frequency is used. However, in high range frequency, several losses may offer such as peak power, switching losses as well as reducing the size of the required battery capacity. In order to avoid the battery's damage, perturb and observe maximum power point tracking algorithm connected with photovoltaic panel is performed. The main objective of this contribution based on proposing a self-correction algorithm to adjust misalignment between primary and secondary coils caused by a random parking of the electric vehicle and to produce suitable input power battery at important frequency level.
Reentrant Condensation and Counterion Distriubtion around Charged Proteins in Solution Studied by ASAXS

A detailed understanding of the ion and counterion distribution and its effect on protein-protein interactions are essential for many biological syst ems. We have performed normal SAXS studies on a model globular protein, bovine serum albumin (BSA ) in solution as a function of protein concentration, ionic strength and also the nature of the added salt [1,2]. We recently observed a reentrant condensation phase behavior for globular proteins in the presence of multivalent cations [2], as shown in Figure 1. Negatively charged globular protein in solution undergoes a phase-separation upon adding trivalent counterions up to a critical concentration C*. Further increasing the salt concentration above a second critical value, C**, causes the precipitate to dissolve and the system turns back to a homogeneous solution [2]. Using normal/anomalous small-angle X-ray scattering (ASAXS), we have also studied the ion distribution around a globular model protein in water [3]. In particular, differences in the ion distribution for diand tri-valent ions have been studied. In this beamtime (14 th May – 22 May 2009), we study the protein-protein interactions in the re-entrant regime as well as the counterion distribution around charged proteins in solution by ASAXS. In order to improve the sensitivity and resolution for ASAXS measurements, a Pilatus 300k detector was borrowed from S.V. Roth's MINAXS beamline.
Using map tasks to investigate the effect of contrastive focus on the Mandarin alveolar-retroflex contrast

A series of map tasks were designed to investigate whether vowel contexts and prosodic prominence may affect the realizations of the alveolar and retroflex sibilants in Beijing Mandarin and Taiwan Mandarin. Results show that the realizations of the sibilants and their contrast varied by vowel context for most speakers, and were selectively subject to prosodic conditioning for only some speakers. The /u/ vowel context was where the alveolar-retroflex contrast was the least distinct and where an enhanced place contrast was achieved for half of the Beijing Mandarin speakers under focus condition. On the other hand, /u/ was the context where some Taiwan Mandarin speakers showed confusion over the place distinction or hypercorrected in response to focal prominence.
Development of high voltage pulse inducement method for biological cell

Electroporation (EP) system is a process of controlling cell functions by using electromagnetic fields (EMF) to create pores through a cellular membrane that causes cell lysis and apoptosis. In this paper we present an experimental setup for fundamental studies on cell EP. An adjustable high voltage pulse generator (3kV/10μs - 600μs pulse length) system were connected to the EP chamber which subsequently allow real time observation of membrane permeability changes and cellular physiology. In order to initiate higher cell viability rate, high transfection efficiency, lower sample contamination and smaller Joule heating the modification of EP chamber need to be implemented. Following that, HeLa cell culture has been projected as cell that will be used in this study. Finally, some suggestions are proposed for the future studies.
Imaging Adult Zebrafish Brain Structures Using Micro-fabricated RF Coil on 3T MRI System

This study introduced a localized approach for magnetic resonance microscopy (MRM) of adult zebrafish brain on our 3T MRI system. A micro-fabricated single-channel radiofrequency (RF) receiver coil was designed by using electromagnetic simulation. Using transmit-only and receive-only (TORO) configuration, receive-only surface coil can achieve high signal-to-noise ratio (SNR) at localized brain regions. To demonstrate the capability, high-resolution MRI of the zebrafish brain with a spatial resolution of 78 times 78 times 500 mum was acquired. The advantages of using micro-fabricated coils on microscopy and molecular imaging were discussed.
A Storm-Based Tag Cloud Platform for Multiple SNS Users

In general, social network service (SNS) has many difficulties in collecting, storing, and analyzing the data in real time because it has the characteristic of big data generated quickly by combining structured and unstructured data. In this paper, we propose a scalable visualization technique that can be applied to real-time SNS data analysis. We first draw out the problems of the existing SNS visualization system and then define the requirements to solve those problems. For resolving these requirements, we use Apache Storm to collect and aggregate Tweet SNS data, which are generated at a high speed, and we visualize the aggregated result in a dynamic tag cloud. To do this, we design and implement a Web interface that allows multiple users to input keywords and visualize their aggregate results in real time. Also, we empirically compare the results of dynamic tag clouds to ensure that they are visualized correctly. Through this research, the users can intuitively understand how the topics of interest are changing in SNS in real time, and the visualization results can be applied to other useful services such as subject trend analysis and customer needs identification.
Study on life cycle of a sporogenous probiotic bacterium in mammalian gastrointestinal tract with image processing analysis

During different phases of growth cycle, Bacillus coagulans RK-02, a sporogenous probiotic bacterium, exhibits different morphological characteristics. Sequential morphological changes of the bacterium, when grown in a 2 L bioreactor in batch mode, were captured under microscope. Processing of the microscopic images and subsequent computational analysis to extract characteristic features, strictly in numerical values, elucidated a time course of quantitative changes in the cell morphology during batch cultivation. This information was further exploited in deciphering different state of growth of the probiotic bacterium across a pH gradient while passing through gastrointestinal tract (GIT) in mouse model. This study would thus help us to understand the kinetics of growth of B. coagulans RK-02 in mouse GIT and consequently decide the dosage regimen of the probiotic.
Treatment and outcome of dogs with leptospirosis: 36 cases (1990-1998).

OBJECTIVE To characterize serologic and clinical features and outcome of dogs with leptospirosis that were treated conservatively (i.e., medical management alone) or with hemodialysis. DESIGN Retrospective study. ANIMALS 36 dogs with leptospirosis. PROCEDURE History; results of physical examinations, ultrasonography, and serologic, hematologic, and serum biochemical analyses; time to resolution of azotemia; and outcome were obtained from medical records. Dogs were treated conservatively (n = 22) or with hemodialysis (14). RESULTS Between 1990 and 1998, amount of rainfall was positively correlated with number of cases of leptospirosis identified per year. Serum antibodies against 6 Leptospira serovars were measured, and titers were highest to Leptospira pomona in 16 (44%) dogs, L bratislava in 9 (25%) dogs, and L hardjo in 1 (3%) dog. Eight (22%) dogs had equally high titers to L pomona and L bratislava, 1 (3%) had equally high titers to L grippotyphosa and L canicola, and 1 (3%) had high titers to L grippotyphosa, L pomona, L canicola, and L bratislava. During initial evaluation, all dogs were azotemic. Thirty (83%) dogs survived, including 12 of 14 (86%) dogs treated with hemodialysis and 18 of 22 (82%) treated conservatively. Serum creatinine concentration was similar in both groups after resolution of clinical signs. CONCLUSIONS AND CLINICAL RELEVANCE Infection with L pomona and L bratislava was recognized as a cause of leptospirosis in dogs, and resulted in development of acute renal failure with various degrees of azotemia. Prognosis for dogs with mild to moderate azotemia was good with conservative treatment, whereas treatment with hemodialysis appeared to improve prognosis for dogs with severe azotemia.
A Fault Tolerant Congestion Aware Routing Protocol for Mobile Adhoc Networks

Problem statement: The performance of ad hoc routing protocols will si gnificantly degrade when there are faulty nodes in the network. Packet losses and bandwidth degradation are caused due to congestion and thus, time and energy is wasted during its recovery. The fault tolerant congestion aware routing protocol addresses these p roblems by exploring the network redundancy through multipath routing. Approach: In this study, it is proposed to design a fault to lerant congestion aware multi path routing protocol to reduce the rou te breakages and congestion losses. The AOMDV protocol is used as a base for the multipath routin g. This proposed scheme enables more nodes to salvage a dropped packet. Results: Simulation results show that the proposed protocol achieves better throughput and packet delivery ratio with reduced d elay, packet drop and energy. Conclusion: An effective congestion control technique proposed in this study proactively detects node level and link level congestion and performs congestion control us ing the fault-tolerant multiple paths.
Natural killer (NK) cells and anti‐tumor therapeutic mAb: unexplored interactions

Tumor‐targeting mAb are widely used in the treatment of a variety of solid and hematopoietic tumors and represent the first immunotherapeutic approach successfully arrived to the clinic. Nevertheless, the role of distinct immune mechanisms in contributing to their therapeutic efficacy is not completely understood and may vary depending on tumor‐ or antigen/antibody‐dependent characteristics. Availability of next‐generation, engineered, tumor‐targeting mAb, optimized in their capability to recruit selected immune effectors, re‐enforces the need for a deeper understanding of the mechanisms underlying anti‐tumor mAb functionality. NK cells participate with a major role to innate anti‐tumor responses, by exerting cytotoxic activity and producing a vast array of cytokines. As the CD16 (low‐affinity FcγRIIIA)‐activating receptor is expressed on the majority of NK cells, its effector functions can be ideally recruited against therapeutic mAb‐opsonized tumor cells. The exact role of NK cells in determining therapeutic efficacy of tumor‐targeting mAb is still unclear and much sought after. This knowledge will be instrumental to design innovative combination schemes with newly validated immunomodulatory agents. We will summarize what is known about the role of NK cells in therapeutic anti‐tumor mAb therapy, with particular emphasis on RTX chimeric anti‐CD20 mAb, the first one used in clinical practice for treating B cell malignancies.
What are the causes of death of patients with tuberculosis? Multiple causes of death in a cohort of cases and a research proposal of presumed causes

The objective of this study was to analyze the multiple causes of death in a cohort of patients with tuberculosis (TB) and to introduce an investigation proposal death for TB from a list of presumable causes. We performed a probabilistic record linkage with the databases of the Information System for Notifiable Diseases (SINAN) 2006 and the Mortality Information System (SIM) 2006-2008. There were 825 deaths, of which 23% for death for TB, deaths due to TB with 16% and 61% without mention of TB. Two hundred and fifteen (42.7%) deaths occurred within the period of treatment, whose profile differed from the pattern of causes when TB was an associated cause, with high frequency of respiratory diseases, AIDS and ill-defined causes. We elaborated a proposal for correction of associated causes of death and an investigation proposal death for TB from a list of presumable causes. According to the proposal, 26 deaths could have modified the underlying cause. This study highlights the importance of record linkage to TB surveillance and improvement of information the SIM and SINAN.
Using Rhetorical Topics for Automatic Summarization

Summarization involves finding the most important information in a text in order to convey the meaning of the document. In this paper, I present a method for using topic information to influence which content is selected for a summary. Texts are divided into topics using rhetorical information that creates a partition of a text into a sequence of non-overlapping topics. To investigate the effect of this topic structure, I compare the output of summarizing an entire text without topics to summarizing individual topics and combining them into a complete summary. The results show that the use of these rhetorical topics improves summarization performance compared to a summarization system that incorporates no topic information, demonstrating the utility of topic structure and rhetorical information for automatic summarization.
Monoclonal antibody MS13 identifies a plasmatocyte membrane protein and inhibits encapsulation and spreading reactions of Manduca sexta hemocytes.

Lepidopterans generally can successfully defend themselves against a variety of parasites or parasitoids. One mechanism they use is to encapsulate the invader in many layers of hemocytes. For encapsulation to occur, the hemocytes must attach to the foreign material, spread, and adhere to each other. The molecules that mediate these processes are not known. One method to identify proteins potentially necessary for adhesion, spreading, and, thus, encapsulation is to use monoclonal antibodies that interfere with these functions. In this paper, we report that a monoclonal antibody against Manduca sexta plasmatocytes effectively inhibited encapsulation of synthetic beads in vitro and in vivo. Furthermore, it inhibited plasmatocyte spreading in vitro. Other anti-hemocyte antibodies did not have these effects. The plasmatocyte-specific monoclonal antibody, mAb MS13, recognized a protein of approximately 90,000 daltons as indicated by Western blot analysis of hemocyte lysate proteins. The epitope recognized by mAb MS13 was present on the exterior surface of plasmatocytes. Using indirect immunohistochemistry with hemocyte-specific antibodies, we also determined that during encapsulation plasmatocytes were the first cells bound to latex beads and later layers consisted of both plasmatocytes and granular cells. Arch.
Compact all-fiber figure-9 dissipative soliton resonance mode-locked double-clad Er:Yb laser.

The first demonstration of a compact all-fiber figure-9 double-clad erbium-ytterbium laser working in the dissipative soliton resonance (DSR) regime is presented. Mode-locking was achieved using a nonlinear amplifying loop (NALM) resonator configuration. The laser was assembled with an additional 475 m long spool of SMF28 fiber in the NALM loop in order to obtain large net-anomalous cavity dispersion (-10.4 ps2), and therefore ensure that DSR would be the dominant mode-locking mechanism. At maximum pump power (4.78 W) the laser generated rectangular-shaped pulses with 455 ns duration and an average power of 950 mW, which at a repetition frequency of 412 kHz corresponds to a record energy of 2.3 μJ per pulse.
Inhibition of RIG-I-Dependent Signaling to the Interferon Pathway during Hepatitis C Virus Expression and Restoration of Signaling by IKKε

ABSTRACT Interferon (IFN) is one important effector of the innate immune response, induced by different viral or bacterial components through Toll-like receptor (TLR)-dependent and -independent mechanisms. As part of its pathogenic strategy, hepatitis C virus (HCV) interferes with the innate immune response and induction of IFN-β via the HCV NS3/4A protease activity which inhibits phosphorylation of IRF-3, a key transcriptional regulator of the IFN response. In the present study, we demonstrate that inhibition by the protease occurs upstream of the noncanonical IKK-related kinases IKKε and TBK-1, which phosphorylate IRF-3, through partial inhibition of the TLR adapter protein TRIF/TICAM1-dependent pathway. Use of TRIF−/− mouse embryo fibroblasts however revealed the presence of a TRIF-independent pathway involved in IFN induction that was also inhibited by NS3/4A. Importantly, we show that NS3/4A can strongly inhibit the ability of the recently described RIG-I protein to activate IFN, suggesting that RIG-I is a key factor in the TRIF-independent, NS3/4A-sensitive pathway. Expression of IFN signaling components including IKKε, TBK-1, TRIF, and wild type or constitutively active forms of RIG-I in the HCV replicon cells resulted in IFN-β promoter transactivation, with IKKε displaying the highest efficiency. Subsequently, overexpression of IKKε resulted in 80% inhibition of both the positive and negative replicative strands of the HCV replicon. The partial restoration of the capacity of the host cell to transcribe IFN-β indicates that IKKε expression is able to bypass the HCV-mediated inhibition and restore the innate antiviral response.
Prevalence and associated factors of depressive and anxiety symptoms among HIV-infected men who have sex with men in China

ABSTRACT HIV-positive men who have sex with men (HIVMSM) face severe stigma and high levels of stressors, and have high prevalence of mental health problems (e.g., depression and anxiety). Very few studies explored the role of positive psychological factors on mental health problems among HIVMSM. The present study investigated the prevalence of two mental health problems (anxiety and depression), and their associated protective (gratitude) and risk (enacted HIV-related stigma, and perceived stress) factors among HIVMSM in China. A cross-sectional survey was conducted among 321 HIVMSM in Chengdu, China, by using a structured questionnaire. Over half (55.8%) of the participants showed probable mild to severe depression (as assessed by the Center of Epidemiologic Studies Depression scale); 53.3% showed probable anxiety (as assessed by the General Anxiety Disorder scale). Adjusted logistic regression models revealed that gratitude (adjusted odds ratio (ORa = 0.90, 95% confidence intervals (95% CI) = 0.86–0.94) was found to be protective, whilst perceived stress (ORa = 1.17, 95% CI = 1.12–1.22) and enacted stigma (ORa = 7.72, 95% CI = 2.27–26.25) were risk factors of depression. Gratitude (ORa = 0.95, 95% CI = 0.91–0.99) was also found to be protective whilst perceived stress (ORa = 1.19, 95% CI = 1.14–1.24) was a risk factor of anxiety. Gratitude did not moderate the associations found between related factors and poor mental health. It is warranted to promote mental health among HIVMSM, as depression/anxiety was highly prevalent. Such interventions should consider enhancement of gratitude, reduction of stress, and removal of enacted stigma as potential strategies, as such factors were significantly associated with depression/anxiety among HIVMSM.
Immunochemical characterization of P pili from invasive Escherichia coli

P pili (or fimbriae) are present on most pyelonephritogenic Escherichia coli strains, and they mediate binding to erythrocytes and epithelial cells. To determine the antigenic diversity of P pili, we purified the pili from 14 bacteremic E. coli strains which caused mannose-resistant hemagglutination. Pilus preparations consisted of one to three bands in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and ranged in molecular weight from 14,000 to 19,500. There was no single band common to all the strains. An enzyme-linked immunosorbent inhibition assay detected 20 ng of pilus antigen. When four different rabbit antisera were used, only two or fewer heterologous strains could inhibit the enzyme-linked immunosorbent assay. Immunoblots yielded the same results. Protein sequences of four P pili had identical N termini. These results show that despite having identical amino-terminal sequences, P pili are antigenically heterogeneous. The receptor-binding domains which are likely to be identical in all strains must be immunorecessive.
Nutritional status in intensive care patients: Evaluation in 84 unselected patients

A prospective nutritional evaluation of 84 unselected patients admitted to a multidisciplinary ICU was performed using anthropometric measurements, creatinine height index (CHI), and serum protein assays. All values tested were significantly lower than those of 40 healthy controls. A matrix of correlation coefficients showed many similarities among the variables studied. Fatal outcome and poor prognosis indices, such as sepsis and renal failure, were analyzed separately. Anthropometric measurements and CHI were not different in the separate groups. Albumin (Alb) and transferrin (Tr) were not different in patients with or without sepsis. Retinol binding prealbumin was significantly higher in patients with renal failure. Thyroxin-binding prealbumin (TBPA) was significantly lower in all the groups. We emphasize the interest of this rapid turnover protein in evaluating nutritional status. We suggest: (1) a systematic nutritional assessment, and (2) an aggressive nutritional support in the ICU patient.