Miracle-dz/UniFAR-FTUs huggingface dataset:
RNase E levels in Escherichia coli are controlled by a complex regulatory
 system that involves transcription of the rne gene from three promoters

The rne gene of Escherichia coli encodes RNase E, an essential endoribonuclease that is involved in both mRNA decay and rRNA processing. Here we present evidence that the gene is transcribed from three promoters: p1, p2 and p3. The p2 and p3 promoters map 34 and 145 nt upstream from the previously characterized rne promoter, p1, generating unusually long 5′ UTRs of 395 and 506 nt respectively. Based on promoter–lacZ transcriptional fusions, p1 is a more efficient promoter than either p2 or p3. Low copy number or single copy number vectors carrying rne transcribed from either p1, p2 or p3 alone complement the rneΔ1018::bla deletion mutation at 30°C, 37°C and 44°C. However, normal autoregulation requires the presence of all three promoters. A comparison among intracellular levels of RNase E, the half‐lives of the rpsO, rpsT and rne mRNAs, and growth rates, indicates that the cell contains a considerable excess of RNase E protein. In addition, when the rne transcript is stabilized at low RNase E levels, it is not efficiently translated.
Cost function tuning methodology for FCS-MPC applied to PMSM drives

This paper presents a discussion about cost function design procedure for finite control set model predictive control (FCS-MPC) applied to electrical permanent magnet synchronous motor (PMSM) drive. In such analysis, different cost function choices were evaluated, with different type of costs and weighting, in order to achieve the main control objective: minimum torque error, accomplishing the maximum torque per ampere condition. Moreover, this study is completed with discussion on the choice of weighted variables for each objective and its influence in some figures of merit, such as current THD and torque ripple.
Superpipelined adder designs

The superpipelining concept is applied to adder designs. Superpipelined designs of ripple carry, carry select, conditional sum, and carry lookahead adders are presented as examples. It is shown that the carry skip adder cannot be superpipelined. Results for the total number of latches required, the number of pipelining stages, and the total gate counts are presented. It is shown that the superpipelined carry lookahead adder is faster and less complex than the other adders. <<ETX>>
Private Updates to Anonymous Databases

Suppose that Alice, owner of a k-anonymous database, needs to determine whether her database, when adjoined with a tuple owned by Bob, is still k-anonymous. Suppose moreover that access to the database is strictly controlled, because for example data are used for experiments that need to be maintained confidential. Clearly, allowing Alice to directly read the contents of the tuple breaks the privacy of Bob; on the other hand, the confidentiality of the database managed by Alice is violated once Bob has access to the contents of the database. Thus the problem is to check whether the database adjoined with the tuple is still k-anonymous, without letting Alice and Bob know the contents of, respectively, the tuple and the database. In this paper, we propose two protocols solving this problem.
An advanced drain current model for DGMOSFETs including self-heating effects

An advanced drain current model for symmetrical Double-Gate MOSFETs (DGMOSFETs), including short channel, velocity saturation and self-heating effects, is presented. The temperature dependence of the low-field mobility, saturation velocity and inversion charge is analyzed and accurately included in the model. Self-heating is considered through the thermal resistance of the device, which is estimated in two ways: from an equivalent thermal circuit and from numerical output characteristic curves, obtained with a commercial TCAD tool (Sentaurus by Synopsys), and fitted with a drain current model. The validity of the model is checked by comparing with simulation results, for the typical bias range used in integrated circuits.
Immunoglobulin gene segment usage, location and immunogenicity in mutated and unmutated chronic lymphocytic leukaemia

The mutational status of the variable region of the immunoglobulin heavy chain gene (IgVH) is an important prognostic marker in B‐cell chronic lymphocytic leukaemia (B‐CLL), with mutated patients having improved outcome. To examine the impact of mutational status on VH, DH, and JH gene segment location and immunogenicity, we analysed 375 IgH sequences from 356 patients with B‐CLL. Although VH and DH gene usage was different in mutated compared to unmutated patients, there was no impact of gene location on frequency of use or clinical outcome. Surprisingly, somatic mutations did not increase the immunogenicity of the Ig, as assessed by predicted binding affinity of Ig‐derived peptides to major histocompatibility Class I and Class II molecules. Even excluding patients using VH1‐69, cases using the VH1 gene family had a poor outcome. Both mutated and unmutated CLL patients demonstrated evidence of antigen selection. The worst outcome was seen in the subset of 14 unmutated patients with similar HCDR3 amino acid sequence using VH1‐69, DH3‐3 and JH6, suggesting an antigen‐driven process modulating the clinical course.
Comparison of s‐phase fraction, working formulation, and kiel classification in non‐Hodgkin's lymphoma

The prognostic value of S‐phase fraction (SPF), determined by flow cytometric study from paraffin‐embedded tissue, and grading by Working Formulation (WF) and Kiel classification were compared among 245 patients with non‐Hodgkin's lymphoma followed for the median of 89 months or until death. Histologic reclassification and SPF determinations were done without knowledge on clinical data. SPF (P equals 0.0001), WF (P equals 0.0003), and Kiel classification (P equals 0.0008) were associated with mortality in lymphoma in a univariate analysis, and WF and SPF were independent prognostic factors in Cox's multivariate analysis. Although SPF correlated strongly both with WF and Kiel grades (P less than 0.0001), low‐grade and high‐grade malignant lymphomas according to Kiel classification, and highgrade lymphomas according to WF could be divided into groups with significantly different outcome by SPF. The results suggests a role for SPF in therapeutic decision‐making.
Internal water molecules and H‐bonding in biological macromolecules: A review of structural features with functional implications

Conserved structural patterns of internal water molecules and/or H‐bond chains were observed and are here correlated in this review, which then describes two functional properties: equilibration of hydrostatic pressure and proton transport. Available evidence in support of these hypotheses is presented, together with suggested experiments to test them. High‐resolution crystal structures of a variety of proteins were studied with interactive computer graphics. Conserved H‐bonding linkages may be used as a paradigm for a rationalization of proton transport in membranes. The concept of the “proton wire,” which links buried active‐site amino acids with the surface of the protein raises the more general question of the functional role of the various molecular components
Information search for children using Faceted navigation

Information search is one of the most common activities over Internet. Several search engines crawl the web round the clock and fetch useful information according to users' interest. To date, most of these search engines exploit the keyword based searching procedure which might be inappropriate for some naive users such as children. It may be very intricate for children to search their desired content effectively using the traditional `keyword based' search mechanism. They may fail to map the desired concept into appropriate keywords. To circumvent this situation, Faceted navigation is proposed as an effective alternate search method for children. Faceted navigation, also termed as Faceted search, is a specialized form of exploratory search that allows the users to search a domain on the basis of its attributes. We have performed several experiments to compare faceted search to the traditional query-based search mechanism. In particular, a faceted search based test interface has been designed. Children were asked to perform some pre-designated tasks on this system and their performance was analyzed on the said faceted search interface. A quantitative comparison was made with a query based search system using few quantitative performance metrics: keyword and spelling mistakes, number of missed pages and average accuracy. It is evident from experimental results that children performed much better on the proposed faceted search interface than query based search system.
Exploring the Needs of Users for Supporting Privacy-Protective Behaviors in Smart Homes

In this paper, we studied people’s smart home privacy-protective behaviors (SH-PPBs), to gain a better understanding of their privacy management do’s and don’ts in this context. We first surveyed 159 participants and elicited 33 unique SH-PPB practices, revealing that users heavily rely on ad hoc approaches at the physical layer (e.g., physical blocking, manual powering off). We also characterized the types of privacy concerns users wanted to address through SH-PPBs, the reasons preventing users from doing SH-PPBs, and privacy features they wished they had to support SH-PPBs. We then storyboarded 11 privacy protection concepts to explore opportunities to better support users’ needs, and asked another 227 participants to criticize and rank these design concepts. Among the 11 concepts, Privacy Diagnostics, which is similar to security diagnostics in anti-virus software, was far preferred over the rest. We also witnessed rich evidence of four important factors in designing SH-PPB tools, as users prefer (1) simple, (2) proactive, (3) preventative solutions that can (4) offer more control.
Towards Enhancing Empathy Through Emotion Augmented Remote Communication

Our ability to empathize stands at the core of our existence as humans. It has dramatically contributed to our evolution as species and remains key to our relationships with family, friends, and colleagues. Yet, we sometimes find it difficult to empathize, more so in the online space increasingly dominating our interactions. In this work, we explore the potential of videoconferencing platforms as avenues for augmenting empathy. We have developed Project Us, a system that uses machine learning to analyze interlocutors’ tone of voice and facial expressions during online interactions, compiles their emotional valence and feeds it back to each participant as a real-time visual cue. Tested with 40 users, Project Us shows the emergence of empathy-related behaviours, such as a higher awareness of own and other’s emotions, and an increased use of pro-social language, as evaluated through quantitative (natural language processing) and qualitative methods. We also analyze ethical challenges of empathy augmentation.
Ga11y: An Automated GIF Annotation System for Visually Impaired Users

Animated GIF images have become prevalent in internet culture, often used to express richer and more nuanced meanings than static images. But animated GIFs often lack adequate alternative text descriptions, and it is challenging to generate such descriptions automatically, resulting in inaccessible GIFs for blind or low-vision (BLV) users. To improve the accessibility of animated GIFs for BLV users, we provide a system called Ga11y (pronounced “galley”), for creating GIF annotations. Ga11y combines the power of machine intelligence and crowdsourcing and has three components: an Android client for submitting annotation requests, a backend server and database, and a web interface where volunteers can respond to annotation requests. We evaluated three human annotation interfaces and employ the one that yielded the best annotation quality. We also conducted a multi-stage evaluation with 12 BLV participants from the United States and China, receiving positive feedback.
Relevance of DNA Alkylation Damage Repair Systems in Salmonella enterica Virulence

ABSTRACT Systematic inactivation of pathways involved in DNA alkylation damage repair demonstrated that inactivation of the ada, ogt, tag, uvrA, and mfd genes is required to detect a Salmonella enterica virulence decrease. Furthermore, the fitness of S. enterica, defective in these genes, is lowered only when the bacterium is orally, but not intraperitoneally, inoculated.
Characterization of surface antigen on cells infected by fibroma virus.

Cells infected with fibroma virus developed a surface antigen which could be detected by immunofluorescence. Sera from rabbits with regressed fibroma-induced tumors reacted with the surface of viable fibroma-infected cells, but not with cells infected with vaccinia virus or herpesvirus. Serum prepared against vaccinia virus, herpesvirus, SV40 virus and rabbit papilloma virus failed to react with fibroma-infected cells. The surface antigen appeared to be a late antigen and was dependent upon viral DNA synthesis. The antibody reaction was not to intact virions attached to the cell surface. The antigen persisted in association with the cell membrane long after infectious virus had decreased to low levels. A temporal relationship existed between the surface antigen measured by the fluorescent antibody technique and the antigen measured by the macrophage migration-inhibition test. Antibody reactive against the surface antigen developed in rabbits with growing fibromas and the antibody titer increased as the tumors regressed. The possible role of cell-mediated and humoral immune responses against this membrane-associated antigen in tumor regression is discussed.
A ferroelectric capacitor compact model for circuit simulation

A ferroelectric capacitor compact model based on physical and mathematical basis with model parameters extracted from experimental measurements is proposed. This model accounts for both main hysteresis loop and minor hysteresis loops with asymmetric nonperiodic input signals. A compact equivalent circuit of this model is described for circuit simulation. Good agreement was achieved between the measurements and simulation results over a wide range of operation.
Spirituality in Nursing from a Japanese Perspective

The purpose of this study was to explore the concept of spirituality and its expression among persons in a Japanese farming community. It was found that spirituality was described as “living in harmony with nature and surrounding people. ” Common expressions of this spirituality were through faith and ways of worship, prayer, search for inner peace, hope and thanksgiving, including spiritual well-being. The latter was defined as showing thanks to nature, ancestors, and people; caring for surrounding people; and peacefully embracing the concept of death. To provide congruent spiritual care, it was suggested that nurses need to expand their own knowledge and understanding of spirituality; integrate spirituality in their nursing care; and improve communication with their clients and their families.
Discharge Communication in Patients Presenting to the Emergency Department With Chest Pain: Defining the Ideal Content

ABSTRACT In an emergency department (ED), discharge communication represents a crucial step in medical care. In theory, it fosters patient satisfaction and adherence to medication, reduces anxiety, and ultimately promotes better outcomes. In practice, little is known about the extent to which patients receiving discharge information understand their medical condition and are able to memorize and retrieve instructions. Even less is known about the ideal content of these instructions. Focusing on patients with chest pain, we systematically assessed physicians’ and patients’ informational preferences and created a memory aid to support both the provision of information (physicians) and its retrieval (patients). In an iterative process, physicians of different specialties (N = 47) first chose which of 81 items to include in an ED discharge communication for patients with acute chest pain. A condensed list of 34 items was then presented to 51 such patients to gauge patients’ preferences. Patients’ and physicians’ ratings of importance converged in 32 of the 34 items. Finally, three experts grouped the 34 items into five categories: (1) information on diagnosis; (2) follow-up suggestions; (3) advice on self-care; (4) red flags; and (5) complete treatment, from which we generated the mnemonic acronym “InFARcT. ” Defining and structuring the content of discharge information seems especially important for ED physicians and patients, as stress and time constraints jeopardize effective communication in this context. Chest pain accounts for up to 10% of all patient presentations in emergency departments (EDs) (Konkelberg & Esterman, 2003). The majority of these patients will usually be discharged within hours, after exclusion of serious conditions such as myocardial infarction (Goodacre et al., 2011). A comprehensive workup of low- to intermediate-risk patients is not feasible in the ED (Reichlin et al., 2009). Yet many of these patients go on to suffer from repeated episodes of chest pain, associated with anxiety and uncertainty about diagnosis and outcome (Jones & Mountain, 2009). Effective discharge communication, empowering patients to understand and memorize medical information, should therefore be an integral part of patient care. It is a likely contributor to better outcomes (Bishop, Barlow, Hartley, & William, 1997; Kessels, 2003), higher patient satisfaction (Kessels, 2003), better adherence to medication (Cameron, 1996; Kessels, 2003), more adequate disease management, and reduced anxiety (Galloway et al., 1997; Mossman, Boudioni, & Slevin, 1999).
Eph/ephrins and N-cadherin coordinate to control the pattern of sympathetic ganglia

Previous studies have suggested that the segmental pattern of neural-crest-derived sympathetic ganglia arises as a direct result of signals that restrict neural crest cell migratory streams through rostral somite halves. We recently showed that the spatiotemporal pattern of chick sympathetic ganglia formation is a two-phase process. Neural crest cells migrate laterally to the dorsal aorta, then surprisingly spread out in the longitudinal direction, before sorting into discrete ganglia. Here, we investigate the function of two families of molecules that are thought to regulate cell sorting and aggregation. By blocking Eph/ephrins or N-cadherin function, we measure changes in neural crest cell migratory behaviors that lead to alterations in sympathetic ganglia formation using a recently developed sagittal slice explant culture and 3D confocal time-lapse imaging. Our results demonstrate that local inhibitory interactions within inter-ganglionic regions, mediated by Eph/ephrins, and adhesive cell-cell contacts at ganglia sites, mediated by N-cadherin, coordinate to sculpt discrete sympathetic ganglia.
Comparison of Latent Semantic Analysis and Probabilistic Latent Semantic Analysis for Documents Clustering

In this paper we compare usefulness of statistical techniques of dimensionality reduction for improving clustering of documents in Polish. We start with partitional and agglomerative algorithms applied to Vector Space Model. Then we investigate two transformations: Latent Semantic Analysis and Probabilistic Latent Semantic Analysis. The obtained results showed advantage of Latent Semantic Analysis technique over probabilistic model. We also analyse time and memory consumption aspects of these transformations and present runtime details for IBM BladeCenter HS21 machine.
Phospholipid composition of Rickettsia prowazeki grown in chicken embryo yolk sacs

The phospholipid composition and phospholipid fatty acid composition of purified Rickettsia prowazeki were determined. The lipid phosphorous content was 6.8 +/- 1.3 microgram/mg of total rickettsial protein. The major phospholipid was phosphatidylethanolamine (60 to 70%); phosphatidylglycerol constituted 20%, and phosphatidylcholine constituted 15%. Small amounts of phosphatidylserine and cardiolipin were detected. The principal fatty acids were 18:1, 16:1, and 16:0. The fatty acid composition of the phosphatidylcholine in the rickettsial extracts was very different than that of the other rickettsial phosphatides and very similar to that of normal yolk sac phosphatidylcholine. The specific of the phosphatidylcholine of rickettsiae grown in the presence of 32P was markedly lower than that of phosphatidylethanolamine and phosphatidylglycerol. It is suggested that the phosphatidylcholine in the rickettsial extract is yolk sac derived and either tightly absorbed or exchanged into the rickettsial membrane.
Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies

Abstract Novel uses of automated flow cytometry technology for measuring levels of protein markers on thousands to millions of cells are promoting increasing need for relevant, customized Bayesian mixture modelling approaches in many areas of biomedical research and application. In studies of immune profiling in many biological areas, traditional flow cytometry measures relative levels of abundance of marker proteins using fluorescently labeled tags that identify specific markers by a single-color. One specific and important recent development in this area is the use of combinatorial marker assays in which each marker is targeted with a probe that is labeled with two or more fluorescent tags. The use of several colors enables the identification of, in principle, combinatorially increasingly numbers of subtypes of cells, each identified by a subset of colors. This represents a major advance in the ability to characterize variation in immune responses involving larger numbers of functionally differentiated cell subtypes. We describe novel classes of Markov chain Monte Carlo methods for model fitting that exploit distributed GPU (graphics processing unit) implementation. We discuss issues of cellular subtype identification in this novel, general model framework, and provide a detailed example using simulated data. We then describe application to a data set from an experimental study of antigen-specific T-cell subtyping using combinatorially encoded assays in human blood samples. Summary comments discuss broader questions in applications in immunology, and aspects of statistical computation.
Prevalance of antibody to hepatitis B surface antigen in various populations

Sera from individuals with different degrees of exposure to the agent of hepatitis B were tested for antibodies to hepatitis B surface antigen (anti-HB-s) by passive hemagglutination and for hepatitis B surface antigen (HB-s Ag) by radioimmunoassay and immunoelectroosmophoresis. In a plasma fractionation plant, anti-HB-s was detected in 82 percent of workers processing human plasma and 3.3 percent were healthy carriers of the antigen. Fifty-six percent of the workers having only casual contact with plasma processing exhibited anti-HB-s and 24 percent of workers with no contact had anti-HB-s, yet HB-s Ag was not found in either of these two groups of workers. A similar correlation was shown in hospital personnel; 31 percent of employees with direct contact to serum specimens and only 8 percent without direct contact had anti-HB-s. The frequency of HB-s Ag (0.8 percent in patients with disorders not involving the liver; 49.8 percent in patients tentatively diagnosed as viral hepatitis) and anti-HB-s (14.5 percent to 28.5 percent, respectively) in selected groups of hospitalized patients varied greatly. In 508 paid blood donors, anti-HB-s was present in 19.9 percent, whereas it was present in only 6.6 percent of 1,146 volunteer donors. These data demonstrate a correlation between frequency of exposure to human blood or blood products and the prevalence of anti-HB-s.