Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Analysis Revealed Unique Genes as Targets for the Anti-inflammatory Action of Activated Protein C in Human Macrophages

Background Activated protein C (APC) has been introduced as a therapeutic agent for treatment of patients with severe sepsis due to its unique anticoagulant and anti-inflammatory properties in the vascular system. In this study we investigated novel targets for the anti-inflammatory action of APC in human macrophages. Methods Using a genome-wide approach, effects of APC on the expression profile in inflammatory activated human macrophages were analyzed. Results We identified, for the first time, genes that are specifically regulated by APC under inflammatory conditions, such as chromatin binding protein 4B (CHMP4B) and p300/CBP-associated factor (PCAF), thus indicating a role of APC in the epigenetic control of gene transcription. A functional assay showed the influence of APC in the acetyltransferase/deacetylase activity of nuclear extracts from inflamed macrophages. Conclusion Our data sheds new light on APC targets in inflammation and opens new lines of investigation that may be explored in order to further elucidate its unique molecule properties.
A new term-weighting scheme for naïve Bayes text categorization

Purpose – Automatic text categorization has applications in several domains, for example e‐mail spam detection, sexual content filtering, directory maintenance, and focused crawling, among others. Most information retrieval systems contain several components which use text categorization methods. One of the first text categorization methods was designed using a naive Bayes representation of the text. Currently, a number of variations of naive Bayes have been discussed. The purpose of this paper is to evaluate naive Bayes approaches on text categorization introducing new competitive extensions to previous approaches.Design/methodology/approach – The paper focuses on introducing a new Bayesian text categorization method based on an extension of the naive Bayes approach. Some modifications to document representations are introduced based on the well‐known BM25 text information retrieval method. The performance of the method is compared to several extensions of naive Bayes using benchmark datasets designed fo.
Suppressed and oppressed? Edited life histories of Australian female academics 1965-1985

While the experiences of women in higher education have received attention from scholars there is a need for gender to be understood in local and time-bound contexts. For example, to what extent do the lives of female academics in non-elite institutions reflect the careers of those in more prestigious establishments? This article uses edited life histories of a group of women academics who worked at one of Australia's oldest colleges of advanced education during the period 1965-1985 to examine the extent to which their careers reflected the position of women academics generally. The article raises the issue whether gender was the key issue in the experience of academic life for this group of female academics or was rurality and institutional type more important in explaining their academic lives.
The Angular Momentum Distribution of Gas and Dark Matter in Galactic Halos

We report results of a series of nonradiative N-body/SPH simulations in a ΛCDM cosmology, designed to study the growth of angular momentum in galaxy systems. A sample of 41 halos of differing mass and environment were selected from a cosmological N-body simulation of size 32.5 h-1 Mpc and resimulated at higher resolution with the tree-SPH code GADGET. We find that the spin of the baryonic component correlates well with the spin of the dark matter, but there is a misalignment of typically 20° between these two components. The spin of the baryonic component is also on average larger than that of the dark matter component, and we find this effect to be more pronounced at lower redshifts. A significant fraction f of gas has negative angular momentum, and this fraction is found to increase with redshift. This trend can be explained as a result of increasing thermalization of the virializing gas with decreasing redshift. We describe a toy model in which the tangential velocities of particles are smeared by Gaussian random motions. This model is successful in explaining some of the global angular momentum properties, in particular the anticorrelation of f with the spin parameter λ and the shape of the angular momentum distributions (AMDs). We investigate in detail the AMDs of the gas and the dark matter components of the halo. We compare and contrast various techniques to determine the AMDs. We show that the technique of adding thermal velocities to streaming motions (broadening) is unsuitable for making comparisons between gas and dark matter AMDs because the shape of the broadened AMDs is predominantly determined by the dispersion and is insensitive to the underlying nonbroadened AMD. In order to bring both gas and dark matter to the same footing, we smooth the angular momentum of the particles over a fixed number of neighbors. The AMDs obtained by this method have a smooth and extended truncation as compared to earlier methods. We find that an analytical function in which the differential distribution of specific angular momentum j is given by P(j) = [1/jΓ(α)](j)α-1e, where jd = jtot/α, can be used to describe a wide variety of profiles, with just one parameter α. The distribution of the shape parameter α for both gas and dark matter follows roughly a lognormal distribution. The mean and standard deviation of log α for gas are -0.04 and 0.11, respectively. About 90%-95% of halos have α < 1.3, while exponential disks in Navarro-Frenk-White (NFW) halos would require 1.3 < α < 1.6. This implies that a typical halo in simulations has an excess of low angular momentum material as compared to that of observed exponential disks, a result that is consistent with the findings of earlier works. Parameter α for gas is correlated with that for dark matter (DM), but they have a significant scatter ⟨αgas/αDM⟩ = 1.09 ± 0.2. Parameter αgas is also biased toward slightly higher values compared to αDM. The angular momentum in halos is also found to have a significant spatial asymmetry with the asymmetry being more pronounced for dark matter.
Classification of HTTP traffic based on C5.0 Machine Learning Algorithm

Our previous work demonstrated the possibility of distinguishing several kinds of applications with accuracy of over 99%. Today, most of the traffic is generated by web browsers, which provide different kinds of services based on the HTTP protocol: web browsing, file downloads, audio and voice streaming through third-party plugins, etc. This paper suggests and evaluates two approaches to distinguish various HTTP content: distributed among volunteers' machines and centralized running in the core of the network. We also assess accuracy of the global classifier for both HTTP and non-HTTP traffic. We achieved accuracy of 94%, which supposed to be even higher in real-life usage. Finally, we provided graphical characteristics of different kinds of HTTP traffic.
Evolution of the Hepatitis E Virus Polyproline Region: Order from Disorder

ABSTRACT The hepatitis E virus (HEV) polyproline region (PPR) is an intrinsically unstructured region (IDR). This relaxed structure allows IDRs, which are implicated in the regulation of transcription and translation, to bind multiple ligands. Originally the nucleotide variability seen in the HEV PPR was assumed to be due to high rates of insertion and deletion. This study shows that the mutation rate is about the same in the PPR as in the rest of the nonstructural polyprotein. The difference between the PPR and the rest of the polyprotein is due to the higher tolerance of the PPR for substitutions at the first and second codon positions. With this higher promiscuity there is a shift in nucleotide occupation of these codons leading to translation of more cytosine residues: a shift that leads to more proline, alanine, serine, and threonine being encoded rather than histidine, phenylalanine, tryptophan, and tyrosine. This pattern of amino acid usage is typical of proline-rich IDRs. Increased usage of cytosine also leads to >22% of all amino acids in the PPR being prolines. Alignments of PPR sequences from HEV strains representing all genotypes indicate that all zoonotic isolates share an ancestor, and the carboxyl half of the PPR is more tolerant of mutations than the amino half. The evolution of HEV PPR, in contrast with that of the rest of the nonstructural polyprotein, is molded by pressures that lead toward increased proline usage with a corresponding decrease in the usage of aromatic amino acids, favoring formation of IDR structures.
Histopathological Audit of 373 Nononcological Hysterectomies in a Teaching Hospital

Hysterectomy, the most common gynecological surgery, provides a definitive cure to various diseases like DUB (dysfunctional uterine bleeding), leiomyoma, adenomyosis, chronic pelvic pain, prolapse, and malignancy. However, with advent of effective medical and conservative treatment modalities for nononcological causes it is now posing question mark on justification of hysterectomy. Therefore, an audit is required to assess the correlation between preoperative diagnosis and histopathological examination of specimen for justification of the procedure. In this study over period of one year (April 2013 to March 2014) 373 hysterectomies specimens were received in the department of pathology for nononcological causes. The age of patients ranged from 22 to 85 years with mean 45 ± 9.2 years. All cases were divided into five categories on the basis of age and audit was done. In this study the most common finding was leiomyoma (43.7%) followed by adenomyosis (19.3%). Almost 50% of hysterectomies causes were justified as preoperative diagnosis matched with histopathology. Cohen kappa statistics were used to measure agreement between preoperative and postoperative histopathological diagnosis which was found to be fair with κ value being 0.36. This study highlights that regular audit of surgeries can help improve quality of health care services and provide safe conservative option to patients.
Inhibition of Apoptosis by P2Y2 Receptor Activation: Novel Pathways for Neuronal Survival

Cell survival is an essential function in the development and maintenance of the nervous system. We demonstrate here a previously unappreciated role for extracellular nucleotide signaling through the P2Y2 receptor in the survival of neurons: PC12 (pheochromocytoma 12) cells and dorsal root ganglion neurons are protected from serum starvation-induced apoptosis by ATP, UTP, and ATPγS, an effect mediated via P2Y2 receptors, as demonstrated by small interfering RNA and genetic knock-out models. This protection occurs independently of neurophin signaling but requires Src activation of ERK (extracellular signal-regulated kinase) and Akt. Moreover, ATPγS and NGF act synergistically to enhance neuronal survival through enhanced TrkA signaling. The results, which define a novel mechanism for inhibition of apoptosis, implicate parallel, interacting systems—extracellular nucleotides/P2Y2 receptors and neurotrophin/TrkA—to sustain neuronal survival.
4D flow MRI assessment of right atrial flow patterns in the normal heart – influence of caval vein arrangement and implications for the patent foramen ovale

Aim To investigate atrial flow patterns in the normal adult heart, to explore whether caval vein arrangement and patency of the foramen ovale (PFO) may be associated with flow pattern. Materials and Methods Time-resolved, three-dimensional velocity encoded magnetic resonance imaging (4D flow) was employed to assess atrial flow patterns in thirteen healthy subjects (6 male, 40 years, range 25–50) and thirteen subjects (6 male, 40 years, range 21–50) with cryptogenic stroke and patent foramen ovale (CS-PFO). Right atrial flow was defined as vortical, helico-vortical, helical and multiple vortices. Time-averaged and peak systolic and diastolic flows in the caval and pulmonary veins and their anatomical arrangement were compared. Results A spectrum of right atrial flow was observed across the four defined categories. The right atrial flow patterns were strongly associated with the relative position of the caval veins. Right atrial flow patterns other than vortical were more common (p = 0.015) and the separation between the superior and inferior vena cava greater (10±5mm versus 3±3mm, p = 0.002) in the CS-PFO group. In the left atrium all subjects except one had counter-clockwise vortical flow. Vortex size varied and was associated with left lower pulmonary vein flow (systolic r = 0.61, p = 0.001, diastolic r = 0.63 p = 0.002). A diastolic vortex was less common and time-averaged left atrial velocity was greater in the CS-PFO group (17±2cm/sec versus 15±1, p = 0.048). One CS-PFO subject demonstrated vortical retrograde flow in the descending aortic arch; all other subjects had laminar descending aortic flow. Conclusion Right atrial flow patterns in the normal heart are heterogeneous and are associated with the relative position of the caval veins. Patterns, other than ‘typical’ vortical flow, are more prevalent in the right atrium of those with cryptogenic stroke in the context of PFO. Left atrial flow patterns are more homogenous in normal hearts and show a relationship with flow arising from the left pulmonary veins.
Variation in subsurface thermal characteristics of microrefuges used by range core and peripheral populations of the American pika (Ochotona princeps)

Abstract Microrefuges provide microclimates decoupled from inhospitable regional climate regimes that enable range‐peripheral populations to persist and are important to cold‐adapted species in an era of accelerated climate change. However, identifying and describing the thermal characteristics of microrefuge habitats is challenging, particularly for mobile organisms in cryptic, patchy habitats. We examined variation in subsurface thermal conditions of microrefuge habitats among different rock substrate types used by the American pika (Ochotona princeps), a climate‐sensitive, rock‐dwelling Lagomorph. We compared subsurface temperatures in talus and lava substrates in pika survey sites in two US national park units; one park study area on the range periphery and the other in the range core. We deployed paired sensors to examine within‐site temperature variation. We hypothesized that subsurface temperatures within occupied sites and structurally complex substrates would be cooler in summer and warmer in winter than unoccupied and less complex sites. Although within‐site variability was high, with correlations between paired sensors as low as 47%, we found compelling evidence that pikas occupy microrefuge habitats where subsurface conditions provide more thermal stability than in unoccupied microhabitats. The percentage of days in which microhabitat temperatures were between −2.5 and 25.5°C was significantly higher in occupied sites. Interestingly, thermal conditions were substantially more stable (p < .05) in the lava substrate type identified to be preferentially used by pikas (pahoehoe vs. a'a) in a previous study. Our study and others suggest that thermal stability appears to be the defining characteristic of subsurface microrefuges used by American pikas and is a likely explanation for enigmatic population persistence at the range periphery. Our study exemplifies an integrated approach for studying complex microhabitat conditions, paired with site use surveys and contextualized with information about gene flow provided by complementary studies.
An allosteric model of circadian KaiC phosphorylation

In a recent series of ground-breaking experiments, Nakajima et al. [Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, Kondo T (2005) Science 308:414–415] showed that the three cyanobacterial clock proteins KaiA, KaiB, and KaiC are sufficient in vitro to generate circadian phosphorylation of KaiC. Here, we present a mathematical model of the Kai system. At its heart is the assumption that KaiC can exist in two conformational states, one favoring phosphorylation and the other dephosphorylation. Each individual KaiC hexamer then has a propensity to be phosphorylated in a cyclic manner. To generate macroscopic oscillations, however, the phosphorylation cycles of the different hexamers must be synchronized. We propose a novel synchronization mechanism based on differential affinity: KaiA stimulates KaiC phosphorylation, but the limited supply of KaiA dimers binds preferentially to those KaiC hexamers that are falling behind in the oscillation. KaiB sequesters KaiA and stabilizes the dephosphorylating KaiC state. We show that our model can reproduce a wide range of published data, including the observed insensitivity of the oscillation period to variations in temperature, and that it makes nontrivial predictions about the effects of varying the concentrations of the Kai proteins.
Assault, post-traumatic amnesia and other variables related to outcome following head injury

Objective: To estimate how many patients who sustain a head injury might benefit from intervention and support each year and to consider whether relationships can be found between demographic data relating to patients' circumstances at the time of head injury, and their outcomes six months later. Design: Data collected on 625 patients through follow-up interviews and assessments by the Oxford Head Injury Service for a randomized controlled trial of intervention conducted in 1993–94. Setting: A mixed rural and urban Health District with a population of approximately 560 000. Patients: Patients were aged between 16 and 65 years and resident in Oxfordshire. They presented over 13 months to accident and emergency departments, or were admitted to hospital. All were diagnosed as having suffered a head injury. Outcome measures: The Rivermead Head Injury Follow Up Questionnaire and the Rivermead Post Concussion Symptoms Questionnaire. Results: Data are given on age, sex, social circumstances, employment, cause of injury, severity of associated injuries, post-traumatic amnesia (PTA), anticonvulsants, postconcussion symptoms and activities of everyday life. Outcome at six months was significantly worse for those who had been assaulted as against all other causes of injury combined (p = 0.0001); and/or had been admitted to hospital (p = 0.0001); and/or had sustained more severe additional injuries (p = 0.04); and/or had experienced any PTA (p = 0.00001). The minimum incidence of such injuries in those aged 16–65, calculated for Oxfordshire, is 292 per annum (74/100 000 aged 16–65 per year). Conclusions: In the general population 52/100 000 patients per annum will experience more serious head injuries as indicated by hospital admission and/or one or more fractures and/or any length of PTA and/or having been assaulted. This group may benefit from monitoring and support and their needs should be considered when planning services.
Stochastic gradient descent for robust inverse photomask synthesis in optical lithography

Optical lithography is a critical step in the semiconductor manufacturing process, and one key problem is the design of the photomask for a particular circuit pattern, given the optical aberrations and diffraction effects associated with the small feature size. Inverse lithography synthesizes an optimal mask by treating the design as an image synthesis inverse problem. To date, much effort is dedicated to solving it for some nominal process conditions. However, the small feature size also suggests that the effect of process variations is more pronounced. In this paper, we design a mask that is robust against focus variations within the inverse lithography framework. Each iteration involves more computation than a similar method designed for the nominal conditions, but we simplify the task by using stochastic gradient descent, which is a technique from machine learning. Simulation shows that the proposed algorithm is effective in producing robust masks.
Registration of organs with sliding interfaces and changing topologies

Smoothness and continuity assumptions on the deformation field in deformable image registration do not hold for applications where the imaged objects have sliding interfaces. Recent extensions to deformable image registration that accommodate for sliding motion of organs are limited to sliding motion along approximately planar surfaces or cannot model sliding that changes the topological configuration in case of multiple organs. We propose a new extension to free-form image registration that is not limited in this way. Our method uses a transformation model that consists of uniform B-spline transformations for each organ region separately, which is based on segmentation of one image. Since this model can create overlapping regions or gaps between regions, we introduce a penalty term that minimizes this undesired effect. The penalty term acts on the surfaces of the organ regions and is optimized simultaneously with the image similarity. To evaluate our method registrations were performed on publicly available inhale-exhale CT scans for which performances of other methods are known. Target registration errors are computed on dense landmark sets that are available with these datasets. On these data our method outperforms the other methods in terms of target registration error and, where applicable, also in terms of overlap and gap volumes. The approximation of the other methods of sliding motion along planar surfaces is reasonably well suited for the motion present in the lung data. The ability of our method to handle sliding along curved boundaries and for changing region topology configurations was demonstrated on synthetic images.
Outcomes of Shoulder Surgery in the Sitting Position With Interscalene Nerve Block: A Single-Center Series

Background Several case reports have raised serious concerns about the safety of shoulder surgery in the beach-chair position, related to global cerebral hypoperfusion. We summarize our experiences with 15,014 cases of shoulder arthroscopy over an 11-year period. Our primary aim was to evaluate the incidence of intraoperative or immediate postoperative neurologic events and secondarily to relate other perioperative complications. Methods We searched our online deidentified departmental quality improvement and patient safety database for adverse outcomes associated with arthroscopic shoulder surgery performed in the beach-chair position for the 11-year period between April 2001 and November 2011, as well as our hospital-system database and a statewide database. This was compared with the total number of such cases, available from our department billing database. Results The total rate of adverse events was 0.37%. Neurologic abnormalities suggestive of acute cerebral ischemia or hemorrhage did not occur in the immediate perioperative period. One new neurologic deficit was reported, secondary to ischemic stroke, which occurred 24 hours after the surgery. The most frequent complications detected were unplanned return to care (0.067%), local anesthetic systemic toxicity (0.053%), and airway compromise requiring unplanned intubation (0.033%). Complications were infrequent and did not vary in incidence over the course of the study. Conclusions This retrospective study suggests that intraoperative or immediate postoperative stroke is rare when surgery is conducted in beach-chair position in conjunction with regional anesthesia, propofol sedation, and spontaneous respiration via natural airway.