Miracle-dz/UniFAR-FTUs huggingface dataset:
Definition of Herpes Simplex Virus Type 1 Helper Activities for Adeno-Associated Virus Early Replication Events

The human parvovirus Adeno-Associated Virus (AAV) type 2 can only replicate in cells co-infected with a helper virus, such as Adenovirus or Herpes Simplex Virus type 1 (HSV-1); whereas, in the absence of a helper virus, it establishes a latent infection. Previous studies demonstrated that the ternary HSV-1 helicase/primase (HP) complex (UL5/8/52) and the single-stranded DNA-Binding Protein (ICP8) were sufficient to induce AAV-2 replication in transfected cells. We independently showed that, in the context of a latent AAV-2 infection, the HSV-1 ICP0 protein was able to activate rep gene expression. The present study was conducted to integrate these observations and to further explore the requirement of other HSV-1 proteins during early AAV replication steps, i.e. rep gene expression and AAV DNA replication. Using a cellular model that mimics AAV latency and composite constructs coding for various sets of HSV-1 genes, we first confirmed the role of ICP0 for rep gene expression and demonstrated a synergistic effect of ICP4 and, to a lesser extent, ICP22. Conversely, ICP27 displayed an inhibitory effect. Second, our analyses showed that the effect of ICP0, ICP4, and ICP22 on rep gene expression was essential for the onset of AAV DNA replication in conjunction with the HP complex and ICP8. Third, and most importantly, we demonstrated that the HSV-1 DNA polymerase complex (UL30/UL42) was critical to enhance AAV DNA replication to a significant level in transfected cells and that its catalytic activity was involved in this process. Altogether, this work represents the first comprehensive study recapitulating the series of early events taking place during HSV-1–induced AAV replication.
On-line PD detection for condition monitoring of covered-conductor overhead distribution networks-A literature survey

Partial discharge (PD) measurements are universally accepted as an effective and reliable tool for on-line condition monitoring of high voltage (HV) equipment. A relatively new application is the monitoring of falling/leaning trees on the covered-conductor (CC) overhead distribution lines. Rogowski coil is used as a sensor for the detection of PDs produced due to falling trees on the CC overhead lines. This sensor is non-intrusive and superior to the conventional PD detector methods. In the next stage, this wired sensor will be converted into a wireless one. This paper gives the brief introduction to the concept and methodology of PD detection and sensor characteristics for localization of falling trees on the CC lines.
Avian thermoregulation in the heat: scaling of heat tolerance and evaporative cooling capacity in three southern African arid-zone passerines

ABSTRACT Many birds can defend body temperature (Tb) far below air temperature (Ta) during acute heat exposure, but relatively little is known about how avian heat tolerance and evaporative cooling capacity varies with body mass (Mb), phylogeny or ecological factors. We determined maximum rates of evaporative heat dissipation and thermal end points (Tb and Ta associated with thermoregulatory failure) in three southern African ploceid passerines, the scaly-feathered weaver (Sporopipes squamifrons, Mb≈10 g), sociable weaver (Philetairus socius, Mb≈25 g) and white-browed sparrow-weaver (Plocepasser mahali, Mb≈40 g). Birds were exposed to a ramped profile of progressively increasing Ta, with continuous monitoring of behaviour and Tb used to identify the onset of severe hyperthermia. The maximum Ta birds tolerated ranged from 48°C to 54°C, and was positively related to Mb. Values of Tb associated with severe heat stress were in the range of 44 to 45°C. Rates of evaporative water loss (EWL) increased rapidly when Ta exceeded Tb, and maximum evaporative heat dissipation was equivalent to 141–222% of metabolic heat production. Fractional increases in EWL between Ta<40°C and the highest Ta reached by each species were 10.8 (S. squamifrons), 18.4 (P. socius) and 16.0 (P. mahali). Resting metabolic rates increased more gradually with Ta than expected, probably reflecting the very low chamber humidity values we maintained. Our data suggest that, within a taxon, larger species can tolerate higher Ta during acute heat stress. Highlighted Article: Heat tolerance varies with body size in African weavers in the Kalahari Desert.
Improving Named Entity Recognition in Tweets via Detecting Non-Standard Words

Most previous work of text normalization on informal text made a strong assumption that the system has already known which tokens are non-standard words (NSW) and thus need normalization. However, this is not realistic. In this paper, we propose a method for NSW detection. In addition to the information based on the dictionary, e.g., whether a word is out-ofvocabulary (OOV), we leverage novel information derived from the normalization results for OOV words to help make decisions. Second, this paper investigates two methods using NSW detection results for named entity recognition (NER) in social media data. One adopts a pipeline strategy, and the other uses a joint decoding fashion. We also create a new data set with newly added normalization annotation beyond the existing named entity labels. This is the first data set with such annotation and we release it for research purpose. Our experiment results demonstrate the effectiveness of our NSW detection method and the benefit of NSW detection for NER. Our proposed methods perform better than the state-of-the-art NER system.
The LEM3 System for Multitype Evolutionary Optimization

LEM3 is the newest version of the learnable evolution model (LEM), a non-Darwinian evolutionary computation methodology that employs machine learning to guide evolutionary processes. Due to the deep integration of differ- ent modes of operation, several novel elements in its algorithm, and the use of the advanced machine learning system AQ21, the LEM3 system is a highly efficient and effective implementation of the methodology. LEM3 is particularly attractive for multitype optimization because it supports, and treats accordingly, different at- tribute types for describing candidate solutions in the population. These attribute types are nominal, ordinal, structured, cyclic, interval, and ratio. Application to optimization of parameters of a complex system illustrates multitype optimization problem.
The relationship between adiposity and stature in prepubertal children with celiac disease

Abstract Background and aim: The pathogenesis of short stature in celiac disease (CD) is unknown. Obese children are generally taller than their non-obese peers; however, the role of adiposity on stature in CD is unclear. Our aim was to determine the association between adiposity and stature in CD. Subjects and methods: We compared the anthropometric characteristics of prepubertal children of ages 3–12 years, with biopsy-proven CD (n=40) and who were not on gluten-free diet, to same aged, prepubertal non-CD children (n=50). Body mass index (BMI) was calculated using the formula weight/height2. Sex-adjusted midparental target height (MPTH) standard deviation score (SDS) was calculated using National Children Health Statistics data for 18-year-old adults. Data were expressed as mean±standard deviation. Results: CD subjects had significantly lower BMI SDS than controls (0.61±1.22 vs. 1.28±1.60, p=0.027) but were not significantly shorter than the controls (–0.05±1.21 vs. 0.21±1.71, p=0.41). When the patients were subdivided into the normal-weight and overweight/obese groups, the normal-weight CD patients were of similar height as the normal-weight controls (p=0.76) but were significantly shorter than both the overweight/obese controls (p<0.001) and overweight/obese CD children (p<0.001). Interestingly, the overweight/obese CD children were significantly taller than the normal-weight controls (p=0.003). The MPTH SDS did not differ between the groups. Conclusions: Overweight/obese prepubertal children with CD were taller than both their normal-weight CD peers and the normal-weight controls, but were of similar height as the overweight/obese control subjects.
Disinfection of Needleless Catheter Connectors and Access Ports With Alcohol May Not Prevent Microbial Entry: The Promise of a Novel Antiseptic-Barrier Cap

Background. Needleless valve connectors for vascular catheters are widely used throughout the United States because they reduce the risk of biohazardous injuries from needlesticks and exposure to bloodborne pathogens, such as human immunodeficiency virus and hepatitis C virus. Patients with long-term central venous catheters are at significant risk of acquiring catheter-related bloodstream infections caused by microbes that gain access through the connection between the administration set and the catheter or an injection port. Most healthcare practitioners wipe the membranous septum of the needleless connector or the injection port with 70% alcohol before accessing it. We report a simulation study of the efficacy of conventional alcohol disinfection before access, compared with that of a novel antiseptic-barrier cap that, when threaded onto a needleless luer-activated valved connector, allows a chlorhexidine-impregnated sponge to come into continuous contact with the membranous surface; after removal of the cap, there is no need to disinfect the surface with alcohol before accessing it. Methods. One hundred five commercial, needleless luer-activated valved connectors, each accessible by a blunt male-connector luer-lock attachment, were purchased from 3 manufacturers and were tested. The membranous septum of each test device was first heavily contaminated with ~105 colony-forming units of Enterococcus faecalis and then was allowed to dry for 24 hours. Fifteen of the contaminated devices were not disinfected (positive controls), 30 were conventionally disinfected with a commercial 70% alcohol pledget, and 60 had the antiseptic cap threaded onto the connector and then removed after 10 minutes. The test connectors were then accessed with a sterile syringe containing nutrient broth media, which was injected, captured on the downstream side of the intraluminal fluid pathway, and cultured quantitatively. Results. All 15 control connectors (100%) showed massive transmission of microorganisms across the membranous septum (4,500-10,000 colony-forming units). Of the 30 connectors accessed after conventional disinfection with 70% alcohol, 20 (67%) showed transmission of microorganisms (442-25,000 colony-forming units). In contrast, of the 60 connectors cultured after application of the novel antiseptic cap, only 1 (1.6%) showed any transmission of microorganisms (P<.001). Conclusions. The findings of this study show that, if the membranous septum of a needleless luer-activated connector is heavily contaminated, conventional disinfection with 70% alcohol does not reliably prevent entry of microorganisms. In contrast, the antiseptic-barrier cap provided a high level of protection, even in the presence of very heavy contamination. This novel technology deserves to be studied in a clinical trial.
A model for mark size dependence on field emission voltage in heat-assisted magnetic probe recording on CoNi/Pt multilayers

A method of heat-assisted magnetic recording (HAMR) potentially suitable for probe-based storage systems is characterized. In this work, field emission current from a scanning tunneling microscope (STM) tip is used as the heating source. Pulse voltages of 2-7 V with a duration of 500 ns were applied to a CoNi/Pt multilayered film. Different types of Ir/Pt and W STM tips were used in the experiment. The results show that thermally recorded magnetic marks are formed with a nearly uniform mark size of 170 nm when the pulse voltage is above a threshold voltage. The threshold voltage depends on the material work function of the tip, with W having a threshold voltage about 1 V lower than Pt. The emission area of our tip-sample system derived from an analytic expression for field emission current is approximately equal to the mark size, and is largely independent of pulse voltage. This emission area is large compared to lateral heat diffusion in the film. Thus higher applied voltages lead to higher peak temperatures in the model of the write process, but the mark diameter remains relatively unchanged.
Decision-based system identification and adaptive resource allocation

System identification extracts information from a system's operational data to derive a representative model for the system. Studies of system identification have been concentrated on estimation algorithms and their convergence. Focusing on optimal resource allocation under a given reliability requirement, this paper studies identification complexity and its relations to decision making. Dynamic resource assignments are investigated. Resource allocation algorithms are developed and their convergence properties are established. Illustrative examples demonstrate better resource management than worst-case strategies when our algorithms are applied.
Capsaicin Induces Theta-Band Synchronization between Gustatory and Autonomic Insular Cortices

In the insular cortex, the primary gustatory area caudally adjoins the primary autonomic area that is involved in visceral sensory-motor integration. However, it has not been addressed whether neural activity in the gustatory insula (Gu-I) is coordinated with that in the autonomic insula (Au-I). We have demonstrated that TRPV1 activation in Gu-I induces theta-band synchronization between Gu-I and Au-I in rat slice preparations. Electron-microscopic immunohistochemistry revealed that TRPV1 immunoreactivity was much higher in Gu-I than in Au-I, and was mostly detected in dendritic spines receiving asymmetrical synapses. Whole-cell voltage-clamp recordings revealed that, in Gu-I, capsaicin-induced currents in layer 3 (L3) pyramidal cells (PCs) displayed no apparent desensitization, while those in layer 5 (L5) PCs displayed Ca2+-dependent desensitization, suggesting that L3 and L5 PCs respond differentially to TRPV1 activation. Voltage-sensitive dye imaging demonstrated that TRPV1 activation in Gu-I can alter an optical response with a monophasic and columnar temporospatial pattern evoked within Gu-I into an oscillatory one extending over Gu-I and Au-I. Power and cross-power spectral analyses of optical responses revealed theta-band synchronization between Gu-I and Au-I. Whole-cell current-clamp recordings demonstrated that such theta-band waves were mediated by sustained rhythmic firings at 4 and 8 Hz in L3 and L5 PCs, respectively. These results strongly suggested that theta-band oscillatory neural coordination between Gu-I and Au-I was induced by two distinct TRPV1-mediated theta-rhythm firings in L3 and L5 PCs in Gu-I. This network coordination induced by TRPV1 activation could be responsible for autonomic responses to tasting and ingesting spicy foods.
Protein kinase A as a biological target in cancer therapy

Background: cAMP is a second messenger that plays a role in intracellular signal transduction of various stimuli. a major function of cAMP in eukaryotes is activation of cAMP-dependent protein kinase (PKA). PKA is the best understood member of the serine-threonine protein kinase superfamily, and is involved in the control of a variety of cellular processes. since it has been implicated in the initiation and progression of many tumors, PKA has been suggested as a novel molecular target for cancer therapy. Objective/methods: here, after describing some features of cAMP/PKA signaling that are relevant to cancer biology, we review targeting of PKA in cancer therapy, also discussing PKA as a biomarker for cancer detection and monitoring of therapy. Results/conclusions: PKA is an increasingly relevant biological target in the therapy and management of cancer.
Descemet Stripping With Endothelial Keratoplasty for Treatment of Iridocorneal Endothelial Syndrome

Purpose: To describe use of Descemet stripping with endothelial keratoplasty (DSEK) to treat corneal edema associated with iridocorneal endothelial (ICE) syndrome. Methods: In this retrospective, consecutive, interventional case series, the corneal endothelium was selectively replaced by the DSEK technique in eyes with ICE syndrome. Three eyes were treated at 1 center between June 2005 and July 2006. Descemet membrane and endothelium were stripped from the recipient and an 8- or 8.5-mm-diameter donor button consisting of posterior stroma and healthy endothelium was folded and implanted through a 5-mm incision. An air bubble was used to press the donor tissue against the recipient cornea, allowing it to attach without sutures. In 1 case with extensive peripheral anterior synechiae (PAS), after the PAS were broken, the anterior chamber was shallow, so a temporary anchor suture was placed in the peripheral edge of the donor tissue to help ensure that it would unfold in the correct orientation. Results: DSEK successfully resolved corneal edema in 3 male patients with unilateral ICE syndrome who were 47 to 67 years of age. Follow-up ranged from 1 to 14 months. Best spectacle-corrected visual acuity at the most recent visit was 20/20 to 20/30, with a mean refractive cylinder of 1.2 D. Conclusions: Selective replacement of dysfunctional endothelium with DSEK can successfully treat corneal edema and associated visual loss and pain caused by ICE syndrome. Visual recovery is rapid and refractive changes are minimal compared with replacement of the full corneal thickness with a traditional penetrating keratoplasty.
A characterization of the (natural) graph properties testable with one-sided error

The problem of characterizing all the testable graph properties is considered by many to be the most important open problem in the area of property-testing. Our main result in this paper is a solution of an important special case of this general problem; Call a property tester oblivious if its decisions are independent of the size of the input graph. We show that a graph property P has an oblivious one-sided error tester, if and only if P is (semi) hereditary. We stress that any "natural" property that can be tested (either with one-sided or with two-sided error) can be tested by an oblivious tester In particular, all the testers studied thus far in the literature were oblivious. Our main result can thus be considered as a precise characterization of the "natural" graph properties, which are testable with one-sided error. One of the main technical contributions of this paper is in showing that any hereditary graph property can be tested with one-sided error. This general result contains as a special case all the previous results about testing graph properties with one-sided error. These include the results of Goldreich et al., [1998] about testing k-colorability, the characterization of Goldreich and Trevisan [2001] of the graph-partition problems that are testable with 1-sided error, the induced vertex colorability properties of Alon et al., [2000], the induced edge colorability properties of Fischer [2001], a transformation from 2-sided to 1-sided error testing [Goldreich and Trevisan, 2001], as well as a recent result about testing monotone graph properties [Alon and Shapira, 2005]. More importantly, as a special case of our main result, we infer that some of the most well studied graph properties, both in graph theory and computer science, are testable with one-sided error. Some of these properties are the well known graph properties of being perfect, chordal, interval, comparability and more. None of these properties was previously known to be testable.
Studies of Phosphor Concentration and Thickness for Phosphor-Based White Light-Emitting-Diodes

The dependence of luminous efficacy on phosphor concentration and thickness for high-power white light-emitting-diode (WLED) lamps is investigated by employing three-dimensional ray-tracing simulations. The simulations show that the brightness or luminous efficacy of WLED lamps highly depends on the combination of phosphor concentration and phosphor thickness (or phosphor-matrix composite volume). The package with lower concentration and higher phosphor thickness has higher luminous efficacy because the light trapping efficiency is lower with the low phosphor concentration. At the correlated color temperature (CCT) value of around 4000 K, ray-tracing simulation and experimental results show 20% and 23% improvement in lumen, respectively, with a 1.8-mm-phosphor package over a 0.8-mm-phosphor package. A package with convex lens can improve the lumen output over flat lens, but this improvement is small, and it requires higher amount of phosphor, up to 25%, to achieve same CCT value.
Generalized nonlinear timing/phase macromodeling: Theory, numerical methods and applications

We extend the concept of timing/phase macromodels, previously established rigorously only for oscillators, to apply to general systems, both non-oscillatory and oscillatory. We do so by first establishing a solid foundation for the timing/phase response of any nonlinear dynamical system, then deriving a timing/phase macromodel via nonlinear perturbation analysis. The macromodel that emerges is a scalar, nonlinear time-varying equation that accurately characterizes the system's phase/timing responses. We establish strong links of this technique with projection frameworks for model order reduction. We then present numerical methods to compute the phase model. The computation involves a full Floquet decomposition — we discuss numerical issues that arise if direct computation of the monodromy matrix is used for Floquet analysis, and propose an alternative method that are numerically superior. The new method has elegant connections to the Jacobian matrix in harmonic balance method (readily available in most RF simulators). We validate the technique on several highly nonlinear systems, including an inverter chain and a firing neuron. We demonstrate that the new scalar nonlinear phase model captures phase responses under various types of input perturbations, achieving accuracies considerably superior to those of reduced models obtained using LTI/LPTV MOR methods. Thus, we establish a powerful new way to extract timing models of combinatorial/sequential systems and memory (e.g., SRAMs/DRAMs), synchronization systems based on oscillator enslaving (e.g., PLLs, injection-locked oscillators, CDR systems, neural processing, energy grids), signal-processing blocks (e.g., ADCs/DACs, FIR/IIR filters), etc.