Miracle-dz/UniFAR-FTUs huggingface dataset:
Electric Cell-Substrate Impedance Sensing To Monitor Viral Growth and Study Cellular Responses to Infection with Alphaherpesviruses in Real Time

Alphaherpesviruses, including those that commonly infect humans, such as HSV-1 and HSV-2, typically infect and cause cellular damage to epithelial cells at mucosal surfaces, leading to disease. The development of novel technologies to study the cellular responses to infection may allow a more complete understanding of virus replication and the creation of novel antiviral therapies. This study demonstrates the use of ECIS to study various aspects of herpesvirus biology, with a specific focus on changes in cellular morphology as a result of infection. We conclude that ECIS represents a valuable new tool with which to study alphaherpesvirus infections in real time and in an objective and reproducible manner. ABSTRACT Electric cell-substrate impedance sensing (ECIS) measures changes in an electrical circuit formed in a culture dish. As cells grow over a gold electrode, they block the flow of electricity and this is read as an increase in electrical impedance in the circuit. ECIS has previously been used in a variety of applications to study cell growth, migration, and behavior in response to stimuli in real time and without the need for cellular labels. Here, we demonstrate that ECIS is also a valuable tool with which to study infection by alphaherpesviruses. To this end, we used ECIS to study the kinetics of cells infected with felid herpesvirus type 1 (FHV-1), a close relative of the human alphaherpesviruses herpes simplex virus 1 (HSV-1) and HSV-2, and compared the results to those obtained with conventional infectivity assays. First, we demonstrated that ECIS can easily distinguish between wells of cells infected with different amounts of FHV-1 and provides information about the cellular response to infection. Second, we found ECIS useful in identifying differences between the replication kinetics of recombinant DsRed Express2-labeled FHV-1, created via CRISPR/Cas9 genome engineering, and wild-type FHV-1. Finally, we demonstrated that ECIS can accurately determine the half-maximal effective concentration of antivirals. Collectively, our data show that ECIS, in conjunction with current methodologies, is a powerful tool that can be used to monitor viral growth and study the cellular response to alphaherpesvirus infection. IMPORTANCE Alphaherpesviruses, including those that commonly infect humans, such as HSV-1 and HSV-2, typically infect and cause cellular damage to epithelial cells at mucosal surfaces, leading to disease. The development of novel technologies to study the cellular responses to infection may allow a more complete understanding of virus replication and the creation of novel antiviral therapies. This study demonstrates the use of ECIS to study various aspects of herpesvirus biology, with a specific focus on changes in cellular morphology as a result of infection. We conclude that ECIS represents a valuable new tool with which to study alphaherpesvirus infections in real time and in an objective and reproducible manner.
A role for the leucine‐responsive regulatory protein and integration host factor in the regulation of the Salmonella plasmid virulence (spv ) locus in Salmonella typhimurium

The Salmonella plasmid virulence (spv ) genes of Salmonella typhimurium are activated at the level of transcription as the bacteria enter stationary phase in vitro or in response to signals received during intracellular growth. Activation requires the LysR‐like transcription factor SpvR and the alternative sigma factor RpoS. In this report, we show by biochemical and genetic analyses that two chromosomally encoded DNA‐binding proteins contribute to the control of spv expression. These are the integration host factor (IHF), which binds to DNA sequences upstream of the spvR regulatory gene, and the leucine‐responsive regulatory protein (Lrp), which binds to sequences upstream of the spvABCD operon. Under all conditions tested, inactivation of IHF expression reduces the level of spvR transcription by twofold. It also alters the response of the spv regulon to loss of DNA gyrase activity, consistent with a role for IHF in organizing DNA structure in the vicinity of the spvR promoter. Lrp represses spvA gene expression by up to fivefold and Lrp‐mediated repression is antagonized by leucine. The Lrp binding site upstream of the spvA gene overlaps one of the binding sites for the positive regulator SpvR, suggesting a mechanism by which Lrp repression is exerted. This is a first demonstration of a role for Lrp in controlling genes that are also subject to intracellular regulation. These data show that the spv virulence genes belong simultaneously to several regulons in the cell, raising the possibility that spv expression can be fine‐tuned in response to multiple environmental inputs.
CDK inhibitors: positive and negative regulators of G1-phase progression.

Mitogen-dependent progression through the first gap phase (G1) and initiation of DNA synthesis (S phase) during the mammalian cell division cycle are cooperatively regulated by several classes of cyclin-dependent kinases (CDKs) whose activities are in turn constrained by CDK inhibitors (CKIs). CKIs that govern these events have been assigned to one of two families based on their structures and CDK targets. The first class includes the INK4 proteins (inhibitors of CDK4), so named for their ability to specifically inhibit the catalytic subunits of CDK4 and CDK6. Four such proteins [p16 (Serrano et al. 1993), p15 (Hannon and Beach 1994), p18 (Guan et al. 1994; Hirai et al. 1995), and p19 (Chan et al. 1995; Hirai et al. 1995)] are composed of multiple ankyrin repeats and bind only to CDK4 and CDK6 but not to other CDKs or to D-type cyclins. The INK4 proteins can be contrasted with more broadly acting inhibitors of the Cip/Kip family whose actions affect the activities of cyclin D-, E-, and A-dependent kinases. The latter class includes p21 (Gu et al. 1993; Harper et al. 1993; El-Deiry et al. 1993; Xiong et al. 1993a; Dulic et al. 1994; Noda et al. 1994), p27 (Polyak et al. 1994a,b; Toyoshima and Hunter 1994), and p57 (Lee et al. 1995; Matsuoka et al. 1995), all of which contain characteristic motifs within their amino-terminal moieties that enable them to bind both to cyclin and CDK subunits (Chen et al. 1995, 1996; Nakanishi et al. 1995; Warbrick et al. 1995; Lin et al. 1996; Russo et al. 1996). Based largely on in vitro experiments and in vivo overexpression studies, CKIs of the Cip/Kip family were initially thought to interfere with the activities of cyclin D-, E-, and A-dependent kinases. More recent work has altered this view and revealed that although the Cip/Kip proteins are potent inhibitors of cyclin Eand A-dependent CDK2, they act as positive regulators of cyclin Ddependent kinases. This challenges previous assumptions about how the G1/S transition of the mammalian cell cycle is governed, helps explain some enigmatic features of cell cycle control that also involve the functions of the retinoblastoma protein (Rb) and the INK4 proteins, and changes our thinking about how either p16 loss or overexpression of cyclin D-dependent kinases contribute to cancer. Here we focus on the biochemical interactions that occur between CKIs and cyclin Dand E-dependent kinases in cultured mammalian cells, emphasizing the manner by which different positive and negative regulators of the cell division cycle cooperate to govern the G1-to-S transition. To gain a more comprehensive understanding of the biology of CDK inhibitors, readers are encouraged to refer to a rapidly emerging but already extensive literature (for review, see Elledge and Harper 1994; Sherr and Roberts 1995; Chellappan et al. 1998; Hengst and Reed 1998a; Kiyokawa and Koff 1998; Nakayama 1998; Ruas and Peters 1998).
Outliers detection method using clustering in buildings data

To achieve energy efficiency in buildings, a lot of raw data is recorded, during the operation of buildings. This recorded raw data is further used for the analysis of the performance of buildings and its different components e.g. Heating, Ventilation and Air-Conditioning (HVAC). To save time and energy it is required to ensure resilience of the data by detecting and replacing outliers (i.e. data samples that are not plausible) in the data before detailed analysis. This paper discusses the steps involved for detecting outliers in the data obtained from absorption chiller using their On/Off state information. It also proposes a method for automatic detection of On/Off and/or Missing Data status of the chiller. The technique uses two layer K-Means clustering for detecting On/Off as well as Missing Data state of the chiller. After automatic detection of the chiller On/Off cycle, a method for outlier detection is proposed using Z-Score normalization based on the On/Off cycle state of chillers and clustering outliers by Expectation Maximization clustering algorithm. Moreover, the results of filling the missing values with regression and linear interpolation for short and long periods are elaborated. All proposed methods are applied to real building data and the results are discussed.
Three Decades of β-Lactamase Inhibitors

SUMMARY Since the introduction of penicillin, β-lactam antibiotics have been the antimicrobial agents of choice. Unfortunately, the efficacy of these life-saving antibiotics is significantly threatened by bacterial β-lactamases. β-Lactamases are now responsible for resistance to penicillins, extended-spectrum cephalosporins, monobactams, and carbapenems. In order to overcome β-lactamase-mediated resistance, β-lactamase inhibitors (clavulanate, sulbactam, and tazobactam) were introduced into clinical practice. These inhibitors greatly enhance the efficacy of their partner β-lactams (amoxicillin, ampicillin, piperacillin, and ticarcillin) in the treatment of serious Enterobacteriaceae and penicillin-resistant staphylococcal infections. However, selective pressure from excess antibiotic use accelerated the emergence of resistance to β-lactam-β-lactamase inhibitor combinations. Furthermore, the prevalence of clinically relevant β-lactamases from other classes that are resistant to inhibition is rapidly increasing. There is an urgent need for effective inhibitors that can restore the activity of β-lactams. Here, we review the catalytic mechanisms of each β-lactamase class. We then discuss approaches for circumventing β-lactamase-mediated resistance, including properties and characteristics of mechanism-based inactivators. We next highlight the mechanisms of action and salient clinical and microbiological features of β-lactamase inhibitors. We also emphasize their therapeutic applications. We close by focusing on novel compounds and the chemical features of these agents that may contribute to a “second generation” of inhibitors. The goal for the next 3 decades will be to design inhibitors that will be effective for more than a single class of β-lactamases.
Lead-free high-frequency linear-array transducer (30 MHz) for in vivo skin imaging

This work presents the fabrication of a 30 MHz, linear-array transducer based on a KN, 1-3 piezocomposite. Performances of the transducer were characterized and compared to a PZT-based linear array with similar structure. The composites were designed to minimize lateral modes of vibration which can severely degrade imaging performances. Fabrication steps were optimized to achieve a 40 MHz resonant frequency in air with a composite thickness of 69 μm. The measured thickness coupling factor was around 50%. A 128-element, linear array was then fabricated with 100 μm pitch and 1.5 mm elevation aperture. The structure of the transducer (backing, matching layers, and electric components) was optimized to deliver good fractional bandwidth and sensitivity. The final probe was integrated in a prototype, real-time, 128-channel scanner to acquire high-resolution images of the human skin in vivo. Results showed that, compared to PZT ceramics, KN single crystals provide low density and high acoustic velocity, both highly desirable for the manufacturing of HF transducers. The central frequency of the linear-array transducer was 30 MHz despite the KN composite being 20% thicker than equivalent PZT-based composites, and the relative bandwidth was about 50%. High-resolution images of the human skin were acquired and detailed features could be visualized.
Reducing Emergency Department Visits for Acute Gastrointestinal Illnesses in North Carolina (USA) by Extending Community Water Service

Background: Previous analyses have suggested that unregulated private drinking water wells carry a higher risk of exposure to microbial contamination than regulated community water systems. In North Carolina, ~35% of the state’s population relies on private wells, but the health impact associated with widespread reliance on such unregulated drinking water sources is unknown. Objectives: We estimated the total number of emergency department visits for acute gastrointestinal illness (AGI) attributable to microbial contamination in private wells in North Carolina per year, the costs of those visits, and the potential health benefits of extending regulated water service to households currently relying on private wells for their drinking water. Methods: We developed a population intervention model using 2007–2013 data from all 122 North Carolina emergency departments along with microbial contamination data for all 2,120 community water systems and for 16,138 private well water samples collected since 2008. Results: An estimated 29,400 (95% CI: 26,600, 32,200) emergency department visits per year for acute gastrointestinal illness were attributable to microbial contamination in drinking water, constituting approximately 7.3% (95% CI: 6.6, 7.9%) of all AGI-related visits. Of these attributable cases, 99% (29,200; 95% CI: 26,500, 31,900) were associated with private well contamination. The estimated statewide annual cost of emergency department visits attributable to microbiological contamination of drinking water is 40.2 million USD (95% CI: 2.58 million USD, 193 million USD), of which 39.9 million USD (95% CI: 2.56 million USD, 192 million USD) is estimated to arise from private well contamination. An estimated 2,920 (95% CI: 2,650, 3,190) annual emergency department visits could be prevented by extending community water service to 10% of the population currently relying on private wells. Conclusions: This research provides new evidence that extending regulated community water service to populations currently relying on private wells may decrease the population burden of acute gastrointestinal illness. Citation: DeFelice NB, Johnston JE, Gibson JM. 2016. Reducing emergency department visits for acute gastrointestinal illnesses in North Carolina (USA) by extending community water service. Environ Health Perspect 124:1583–1591; http://dx.doi. org/10.1289/EHP160
Role of the C terminus of the ribonucleotide reductase large subunit in enzyme regeneration and its inhibition by Sml1

Ribonucleotide reductase maintains cellular deoxyribonucleotide pools and is thus tightly regulated during the cell cycle to ensure high fidelity in DNA replication. The Sml1 protein inhibits ribonucleotide reductase activity by binding to the R1 subunit. At the completion of each turnover cycle, the active site of R1 becomes oxidized and subsequently regenerated by a cysteine pair (CX2C) at its C-terminal domain (R1-CTD). Here we show that R1-CTD acts in trans to reduce the active site of its neighboring monomer. Both Sml1 and R1-CTD interact with the N-terminal domain of R1 (R1-NTD), which involves a conserved two-residue sequence motif in the R1-NTD. Mutations at these two positions enhancing the Sml1–R1 interaction cause SML1-dependent lethality. These results point to a model whereby Sml1 competes with R1-CTD for association with R1-NTD to hinder the accessibility of the CX2C motif to the active site for R1 regeneration.
Management of obstructing lesions of the left colon by resection, on-table lavage, and primary anastomosis.

BACKGROUND The purpose of this study was to assess the feasibility and safety of single-stage resection, on-table lavage, and primary anastomosis in patients presenting with obstruction of the left colon. METHODS The outcome of surgery in 73 consecutive patients presenting with obstruction of the left colon during a 5-year period was assessed in terms of perioperative complications and long-term survival. RESULTS Sixty-three patients (86%) underwent single-stage restorative procedures. In this group there were four clinical anastomotic leaks (6%). However, there were no deaths as a result of leakage. There were four deaths (6%) but these were not due to anastomotic leakage. Long-term survival rates compared favorably, stage for stage, with large published series of elective experience. CONCLUSIONS We believe that resection, on-table lavage, and primary anastomosis constitute the operation of choice for most patients with acute obstruction of the left colon.
Integrating Different Organizational Levels in Benthic Biodiversity – Ecosystem Functioning (BEF) Studies

Ruth Gingold1,2,3, Axayacatl Rocha Olivares1, Tom Moens2 and Cedric Hubas3 1Department of Biological Oceanography, Centro de Investigacion Cientifica y de Educacion Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Apdo. Postal 2732, 22860 Ensenada BC 2Ghent University, Department of Biology, Marine Biology Section, Krijgslaan 281/S8, 9000 Gent 3Museum National d’Histoire Naturelle, UMR BOREA 7208, MNHN/CNRS/IRD/UPMC, CP 53, 61 rue Buffon, 75231 Paris Cedex 5 1Mexico 2Belgium 3France
Passive vs. active touch‐induced activity in the developing whisker pathway

The mouse trigeminal (V) system undergoes significant postnatal structural and functional developmental changes. Histological modules (barrelettes, barreloids and barrels) in the brainstem, thalamus and cortex related to actively moved (whisking) tactile hairs (vibrissae) on the face allow detailed studies of development. High‐resolution [3H]2‐deoxyglucose (2DG) emulsion autoradiography with cytochrome oxidase histochemistry was used to analyze neuronal activity changes related to specific whisker modules in the developing and mature mouse V system provoked by passive (experimenter‐induced) and active (animal‐induced) displacements of a single whisker (D4). We tested the hypothesis that neuronal activity patterns change in relation to the onset of active touch (whisking) on postnatal day (P)14. Quantitative image analyses revealed: (i) on P7, when whisker‐like patterns of modules are clear, heightened 2DG activity in all appropriate modules in the brainstem, thalamus and cortex; (ii) on P14, a transitory activity pattern coincident with the emergence of whisking behavior that presages (iii) strong labeling of the spinal V subnucleus interpolaris and barrel cortex produced by single‐whisker‐mediated active touch in adults and (iv) at all above‐listed ages and structures, significant suppression of baseline activity in some modules surrounding those representing the stimulated whisker. Differences in activity patterns before and after the onset of whisking behavior may be caused by neuronal activity induced by whisking, and by strengthening of modulatory projections that alter the activity of subcortical inputs produced by whisking behavior during active touch.
Human immunodeficiency virus type 1 RNA Levels in different regions of human brain: Quantification using real-time reverse transcriptase-polymerase chain reaction

Human immunodeficiency virus type 1 (HIV-1) enters the central nervous system shortly after the infection and becomes localized in different regions of the brain, leading to various neurological abnormalities including motor disorders and neurocognitive deficits. Although HIV-1-associated functional abnormalities of the central nervous system (CNS) can be evaluated during life by using various test batteries, HIV-1 virus concentration in different brain regions can be measured only after death. The tissues obtained at autopsy provide a valuable source for determining the role of various factors, including that of HIV-1 viral load in the CNS, that may contribute to the regional CNS neuropathogenesis. For this study, we obtained from the National Institutes of Health-sponsored National NeuroAIDS Tissue Consortium (NNTC) the tissues from different brain regions collected at autopsy of HIV-1-positive (N = 38) and HIV-negative (N = 11) individuals, with postmortem intervals of 2 to 29 h, and measured HIV-1 RNA concentration in the frontal cortex, frontal cortex area 4, frontal cortex area 6, basal ganglia, caudate nucleus, putamen, globus pallidus, substantia nigra, and cerebrospinal fluid. Because HIV-1+ individuals were infected with the virus for up to 21 years and the majority of them had used highly active antiretroviral therapy (HAART), we used highly sensitive real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay in order to detect a wide dynamic range of HIV-1 RNA with lower detection limit of a single copy. The primers and probes were from the long terminal repeat (LTR) region of HIV genome for achieving higher specificity and sensitivity of detection and amplification. Our results demonstrate a wide variation in the concentration of HIV-1 RNA in different brain regions (5.51 and 8,144,073; log10 0.74 and 6.91 copies/g tissue), and despite the high specificity and sensitivity of this method, viral RNA was not detected in 50% of all the samples, and in 30% to 64% of samples of each region of HIV-1+ individuals. However, the highest concentration of viral RNA was found in the caudate nucleus and the lowest concentration in the frontal cortex and cerebrospinal fluid. The viral RNA was undetectable in all samples of HIV-negative individuals.