Miracle-dz/UniFAR-FTUs huggingface dataset:
Interobserver Agreement in the Reporting of Cervical Biopsy Specimens Obtained From Women Screened by Visual Inspection With Acetic Acid and Hybrid Capture 2

Visual inspection with acetic acid (VIA) and human papillomavirus detection have sensitivity higher than cytology but lower specificity. The high false-positive rate of either test poses a challenge to the colposcopists who obtain biopsies from the innocuous changes and to the pathologists who have to interpret large numbers of specimens that are either normal or have low-grade abnormalities. Interobserver variation in histopathologic interpretations of cervical punch biopsy specimens is high, specially for the lower-grade abnormalities. Use of the modified Bethesda system to report histology in place of the cervical intraepithelial neoplasia (CIN) system has the potential to reduce such variability as there are fewer categories. The present study aimed to assess the interobserver agreement to interpret cervical punch biopsies when both pathologists followed the modified Bethesda classification system and also when one pathologist followed the modified Bethesda classification system and the other followed the CIN classification system. Colposcopy-directed punch biopsies were obtained from VIA and/or Hybrid Capture 2-positive women. The Institute pathologist interpreted the slides using the CIN system. Blinded review was done by 2 external pathologists who independently interpreted cervical punch biopsies using the Bethesda system. The Institute pathologist’s diagnoses based on CIN system were converted post hoc into categories belonging to the Bethesda system for comparison. The overall agreement was poor (&kgr;=0.36). The lowest agreement was observed in the low-grade squamous intraepithelial lesion category (&kgr;=0.23) and the highest in the squamous cell carcinoma category (&kgr;=0.76). The agreement between the reviewers, both of whom used the Bethesda system, was substantial.
Supercritical water gasification of biomass: an experimental study of model compounds and potential biomass feeds

Gasification of biomass in supercritical water is a complex process. In supercritical water ideally the biomass structure and the larger molecules are broken down into smaller, gaseous components under the influence of radicals. However, the biomass is normally fed to the system at low temperature and, hence, should traverse a large temperature range before the supercritical conditions are met. During this warming-up (mostly ionic-) reactions may occur leading to the formation of intermediate compounds which are difficult to gasify, but lead to e.g. carbon formation that can cause blockage of process equipment. In case of uncatalyzed gasification the required temperatures are often above 650 °C and thus far above the supercritical temperature for water (374 °C). Together with the required high operating pressures (above 221 bar), this leads to high demands for the materials of construction and, hence, high costs. Reducing the operating temperature to below 600 °C is, next to maximizing gasification efficiency and minimizing carbon formation, an important target for catalyst development. In this thesis, attractive and relevant biomass feed streams have been used; like (crude) glycerine, a by-product from the biodiesel production, algae slurries and aqueous phases produced during the fast pyrolysis of lignocellulosic biomass as well as the aqueous phase produced during upgrading (by hydrogenation) of the primary pyrolysis oil. Results for these raw materials are presented for both the uncatalyzed gasificaion as well as for gasification in the presence of existing (commercial-) and newly developed (in this project) catalysts. For the model compounds chosen, glycerol and ethylene glycol, significant progress is made in the area of catalyst development and deduction of the prevailing reaction mechanisms. Additionally, a more fundamental study into the effect of the molecular structure of n-alcohols and n-carboxylic acids on the gasification performance is performed.
Torsional properties of bamboo-like structured Cu nanowires

Recently, researchers reported that nanowires (NWs) are often polycrystalline, which contain grain or twin boundaries that transect the whole NW normal to its axial direction into a bamboo like structure. In this work, large-scale molecular dynamics simulation is employed to investigate the torsional behaviours of bamboo-like structured Cu NWs. The existence of grain boundaries is found to induce a considerably large reduction to the critical angle, and the more of grain boundaries the less reduction appears, whereas, the presence of twin boundaries only results in a relatively smaller reduction to the critical angle. The introduction of grain boundaries reduces the torsional rigidity of the NW, whereas, the twin boundaries exert insignificant influence to the torsional rigidity. NWs with grain boundaries are inclined to produce a local HCP structure during loading, and the plastic deformation is usually evenly distributed along the axial axis of the NW. The plastic deformation of both perfect NW and NWs with twin boundaries is dominated by the nucleation and propagation of parallel intrinsic stacking faults. This study will enrich the current understanding of the mechanical properties of NWs, which will eventually shed lights on their applications.
The quasispecies regime for the simple genetic algorithm with roulette wheel selection

Abstract We introduce a new parameter to discuss the behavior of a genetic algorithm. This parameter is the mean number of exact copies of the best-fit chromosomes from one generation to the next. We believe that the genetic algorithm operates best when this parameter is slightly larger than 1 and we prove two results supporting this belief. We consider the case of the simple genetic algorithm with the roulette wheel selection mechanism. We denote by ℓ the length of the chromosomes, m the population size, p C the crossover probability, and p M the mutation probability. Our results suggest that the mutation and crossover probabilities should be tuned so that, at each generation, the maximal fitness multiplied by (1 - p C)(1 - p M)ℓ is greater than the mean fitness.
Tolterodine for the treatment of urge urinary incontinence

Introduction: Overactive bladder (OAB) and its resultant urge urinary incontinence (UUI) are significant problems that medically, psychologically and financially affect people. The constellation of symptoms comprising OAB affects ∼ 16% of the adult population and its prevalence increases with aging. The typical class of medications used to treat OAB is antimuscarinics. Areas covered: OAB medications, with a focus on tolterodine for the treatment of UUI are reviewed. A thorough review of English language literature using EMBASE/Medline and PubMed has been performed. Expert opinion: Tolterodine provides a reasonable starting point when treating patients with OAB and UUI. Efficacy and tolerability are generally comparable between tolterodine and other newer antimuscarinics. Tolterodine is a good option as part of the algorithm in the treatment of OAB and UUI.
Genomic Prediction for Tuberculosis Resistance in Dairy Cattle

Background The increasing prevalence of bovine tuberculosis (bTB) in the UK and the limitations of the currently available diagnostic and control methods require the development of complementary approaches to assist in the sustainable control of the disease. One potential approach is the identification of animals that are genetically more resistant to bTB, to enable breeding of animals with enhanced resistance. This paper focuses on prediction of resistance to bTB. We explore estimation of direct genomic estimated breeding values (DGVs) for bTB resistance in UK dairy cattle, using dense SNP chip data, and test these genomic predictions for situations when disease phenotypes are not available on selection candidates. Methodology/Principal Findings We estimated DGVs using genomic best linear unbiased prediction methodology, and assessed their predictive accuracies with a cross validation procedure and receiver operator characteristic (ROC) curves. Furthermore, these results were compared with theoretical expectations for prediction accuracy and area-under-the-ROC-curve (AUC). The dataset comprised 1151 Holstein-Friesian cows (bTB cases or controls). All individuals (592 cases and 559 controls) were genotyped for 727,252 loci (Illumina Bead Chip). The estimated observed heritability of bTB resistance was 0.23±0.06 (0.34 on the liability scale) and five-fold cross validation, replicated six times, provided a prediction accuracy of 0.33 (95% C.I.: 0.26, 0.40). ROC curves, and the resulting AUC, gave a probability of 0.58, averaged across six replicates, of correctly classifying cows as diseased or as healthy based on SNP chip genotype alone using these data. Conclusions/Significance These results provide a first step in the investigation of the potential feasibility of genomic selection for bTB resistance using SNP data. Specifically, they demonstrate that genomic selection is possible, even in populations with no pedigree data and on animals lacking bTB phenotypes. However, a larger training population will be required to improve prediction accuracies.
VEGF and endothelial guidance in angiogenic sprouting

The cellular actions of VEGF need to be coordinated to guide vascular patterning during sprouting angiogenesis. Individual endothelial tip cells lead and guide the blood vessel sprout, while neighboring stalk cells proliferate and form the vascular lumen. Recent studies illustrate how endothelial DLL4/NOTCH signalling, stimulated by VEGF, regulates the sprouting response by limiting tip cell formation in the stalk. The spatial distribution of VEGF, in turn, regulates the shape of the ensuing sprout by directing tip cell migration and determining stalk cell proliferation.
Unique Features of HIV-1 Spread through T Cell Virological Synapses

The spread of viral infections can be initiated by the release of cell-free virus particles that infect at a distance or via cell-associated virus, which can promote the direct transmission of viruses between adjacent cells. In the case of human immunodeficiency virus type 1 (HIV-1), cell–cell contact has been found to enhance infection through specialized structures called virological synapses (VS). Cell–cell interactions between virus scavenging dendritic cells and T cells or between infected and uninfected T cells are two major cell interactions that enhance HIV infection. Here we review the features of VS formed between infected and uninfected T cells and focus on how these differ from infection by cell-free virus. While virus particle production is a shared characteristic of both cell-free and cell–cell HIV transmission, cell–cell infection displays several unique features that contribute to the enhanced efficiency of this mode of transmission. Five distinguishing features of HIV spread through T cell virological synapses are discussed below.
Spectroscopy with electronic terahertz techniques

We report gas absorption spectra and energetic material reflection spectra measured with an all-electronic terahertz (THz) spectrometer. This instrument uses phase-locked microwave sources to drive picosecond GaAs nonlinear transmission lines, enabling measurement of both broadband spectra and single lines with hertz-level precision, a new mode of operation not readily available with optoelectronic THz techniques. We take two approaches to coherent measurements: (1) spatially combining the freely propagating beams from two coherent picosecond pulse generators, or (2) using a more conventional coherent source/detector arrangement with sampling detectors. The first method employs a dual-source interferometer modulating each harmonic of one source with a precisely-offset harmonic from the other source - both sources being driven with stable phase-locked synthesizers - the resultant beat frequency can be low enough for detection by a standard composite bolometer. Room-temperature detection possibilities for the DSI include antenna-coupled Schottky diodes. Finally, we have recently introduced a reflectometer based on serrodyne modulation of a linearized delay line, using a technique that is process-compatible with pulse generator circuits.
Domination Game and an Imagination Strategy

The domination game played on a graph $G$ consists of two players, Dominator and Staller, who alternate taking turns choosing a vertex from $G$ such that whenever a vertex is chosen by either player, at least one additional vertex is dominated. Dominator wishes to dominate the graph in as few steps as possible, and Staller wishes to delay the process as much as possible. The game domination number $\gamma_g(G)$ (resp., $\gamma_g'(G)$) is the number of vertices chosen when Dominator (resp., Staller) starts the game. An imagination strategy is developed as a general tool for proving results on the domination game. We show that for any graph $G$, $\gamma(G)\leq\gamma_g(G)\leq2\gamma(G)-1$, and that all possible values can be realized. It is proved that for any graph $G$, $\gamma_g(G)-1\leq\gamma'_g(G)\leq\gamma_g(G)+2$, and that most of the possibilities for mutual values of $\gamma_g(G)$ and $\gamma_g'(G)$ can be realized. A connection with Vizing's conjecture is established, and a lower bound on the game domination number of an arbitrary Cartesian product is proved. Several problems and conjectures are also stated.
Tapentadol extended-release for treatment of chronic pain: a review

Tapentadol is a centrally acting analgesic with a dual mechanism of action of mu receptor agonism and norepinephrine reuptake inhibition. Tapentadol immediate-release is approved by the US Food and Drug Administration for the management of moderate-to-severe acute pain. It was developed to decrease the intolerability issue associated with opioids. Tapentadol extended-release has a 12-hour duration of effect, and has recently been evaluated for pain in patients with chronic osteoarthritis, low back pain, and pain associated with diabetic peripheral neuropathy. Tapentadol extended-release was found to provide safe and highly effective analgesia for the treatment of chronic pain conditions, including moderate-to-severe chronic osteoarthritis pain and low back pain. Initial trials demonstrating efficacy in neuropathic pain suggest that tapentadol has comparable analgesic effectiveness and better gastrointestinal tolerability than opioid comparators, and demonstrates effectiveness in settings of inflammatory, somatic, and neuropathic pain. Gastrointestinal intolerance and central nervous system effects were the major adverse events noted. Tapentadol will need to be rigorously tested in chronic neuropathic pain, cancer-related pain, and cancer-related neuropathic pain.
Efficient user-space protocol implementations with QoS guarantees using real-time upcalls

Two important requirements for protocol implementations to be able to provide quality of service (QoS) guarantees within the endsystem are: (1) efficient processor scheduling for application and protocol processing and (2) efficient mechanisms for data movement. Scheduling is needed to guarantee that the application and protocol tasks involved in processing each stream execute in a timely manner and obtain their required share of the CPU. We have designed and implemented an operating system (OS) mechanism called the real-time upcall (RTU) to provide such guarantees to applications. The RTU mechanism provides a simple real-time concurrency model and has minimal overheads for concurrency control and context switching compared to thread-based approaches. To demonstrate its efficacy, we have built RTU-based transmission control protocol (TCP) and user datagram protocol (UDP) protocol implementations that combine high efficiency with guaranteed performance. For efficient data movement, we have implemented a number of techniques such as: (1) direct movement of data between the application and the network adapter; (2) batching of input-output (I/O) operations to reduce context switches; and (3) header-data splitting at the receiver to keep bulk data page aligned. Our RTU-based user-space TCP/Internet protocol (TCP/IP) implementation provides bandwidth guarantees for bulk data connections even with real-time and "best-effort" load competing for CPU on the endsystem. Maximum achievable throughput is higher than the NetBSD kernel implementation due to efficient data movement. Sporadic and small messages with low delay requirements are also supported using reactive RTUs that are scheduled with very low delay. We believe that ours is the first solution that combines good data path performance with application-level bandwidth and delay guarantees for standard protocols and OSs.
Higher Serum Levels of Free ĸ plus λ Immunoglobulin Light Chains Ameliorate Survival of Hemodialysis Patients

Background/Aims: Impaired immune function is common in patients with chronic renal failure. Now, we determined whether serum levels of free immunoglobulin light chains predict mortality in patients with chronic kidney disease stage 5 on hemodialysis. Methods: We performed a prospective cohort study of 160 hemodialysis patients with a median follow-up of 15 months (interquartile range, 3–44 months). Serum levels of free ĸ and λ immunoglobulin light chains were measured at the start of the study. The primary end point was mortality from any cause. Results: In survivors, median serum levels of free ĸ plus λ immunoglobulin light chains were significantly higher compared with nonsurvivors (p < 0.05). Survival was significantly longer in those patients who had serum levels of free ĸ plus λ immunoglobulin light chains above the median compared with patients with serum levels below the median of 210 mg/l (χ2 = 5.91; p = 0.015 by log-rank, Mantel-Cox, test). We performed univariate and multivariate regression analysis showing that older age and lower serum levels of free ĸ plus λ immunoglobulin light chains predicted mortality in hemodialysis patients. Conclusion: Higher serum levels of free ĸ plus λ immunoglobulin light chains ameliorate survival in hemodialysis patients.
On fault tolerant ad hoc network design

Minimal configuration and quick deployment of ad hoc networks make it suitable for numerous applications such as emergency situations, border monitoring, and military missions, etc. For such ad hoc networks to fulfill their mission in a timely manner, they should be able to establish a connection between nodes and to maintain this connection until the communication halts. Establishing a connection is achieved by using a routing protocol, and maintaining it is achieved by having a resilient fault tolerant network. In this paper, we propose a network design scheme that incorporates these features. We first propose a special network topology that is unique in terms of how nodes are interconnected. After constructing the initial topology, we propose a distributed routing protocol that allows any two sites to communicate by traversing at most 2 nodes regardless of the network size. We conducted both simulation study and theoretical analysis; the results show that the proposed scheme is resilient to network dynamics and has high quality as well as efficient routing.
The histone H1 family: specific members, specific functions?

Abstract The linker histone H1 binds to the DNA entering and exiting the nucleosomal core particle and has an important role in establishing and maintaining higher order chromatin structures. H1 forms a complex family of related proteins with distinct species, tissue and developmental specificity. In higher eukaryotes all H1 variants have the same general structure, consisting of a central conserved globular domain and less conserved N-terminal and C-terminal tails. These tails are moderately conserved among species, but differ among variants, suggesting a specific function for each H1 variant. Due to compensatory mechanisms and to the lack of proper tools, it has been very difficult to study the biological role of individual variants in chromatin-mediated processes. Our knowledge about H1 variants is indeed limited, and in vitro and in vivo observations have often been contradictory. Therefore, H1 variants were considered to be functionally redundant. However, recent knockout studies and biochemical analyses in different organisms have revealed exciting new insights into the specificity and mechanisms of actions of the H1 family members. Here, we collect and compare the available literature about H1 variants and discuss possible specific roles that challenge the concept of H1 being a mere structural component of chromatin and a general repressor of transcription.
Reminiscence, Digital Storytelling and Maps: How Technology Affects Loneliness of Older Adults

Issues related to social isolation, loneliness and reminiscing are vital for the elderly, especially for those who suffer from memory loss or live far from their families and friends. Through this research as a PhD student, I will examine the effects of specific technologies (social networking sites, chatbots and online maps) on the elderly’s feelings of loneliness under the scope of reminiscing and online storytelling. Three distinct communication technologies will be implemented: a chatbot, Facebook posts and a cooperative online map where users can post, read and make comments on geo­tagged personal stories. The methodology of this experimental study implements both qualitative (semi­structured in­depth interviews) and quantitative techniques (structured questionnaires, log files) for data collection.
Central projections of lagenar primary neurons in the chick

Perception of linear acceleration and head position is the function of the utricle and saccule in mammals. Nonmammalian vertebrates possess a third otolith endorgan, the macula lagena. Different functions have been ascribed to the lagena in arboreal birds, including hearing, equilibrium, homing behavior, and magnetoreception. However, no conclusive evidence on the function of the lagena in birds is currently available. The present study is aimed at providing a neuroanatomical substrate for the function of the lagena in the chicken as an example of terrestrial birds. The afferents from the lagena of chick embryos (E19) to the brainstem and cerebellum were investigated by the sensitive lipophilic tracer Neuro Vue Red in postfixed ears. The results revealed that all the main vestibular nuclei, including the tangential nucleus, received lagenar projections. No lagenar terminals were found in auditory centers, including the cochlear nuclei. In the cerebellum, the labeled terminals were found variably in all of the cerebellar nuclei. In the cerebellar cortex, the labeled fibers were found mostly in the uvula, with fewer afferents in the flocculus and paraflocculus. None was seen in the nodulus. The absence of lagenar afferent projections in auditory nuclei and the presence of a projection pattern in the vestibular nuclei and cerebellum similar to that of the utricle and saccule suggest that the primary role of the lagena in the chick lies in the processing of vestibular information related to linear acceleration and static head position. J. Comp. Neurol. 521:3524‐3540, 2013. © 2013 Wiley Periodicals, Inc.