Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth kinetics of individual Bacillus subtilis cells and correlation with nucleoid extension

The growth rate of individual cells of Bacillus subtilis (doubling time, 120 min) has been calculated by using a modification of the Collins-Richmond principle which allows the growth rate of mononucleate, binucleate, and septate cells to be calculated separately. The standard Collins-Richmond equation represents a weighted average of the growth rate calculated from these three major classes. Both approaches strongly suggest that the rate of length extension is exponential. By preparing critical-point-dried cells, in which major features of the cell such as nucleoids and cross-walls can be seen, it has also been possible to examine whether nucleoid extension is coupled to length extension. Growth rates for nucleoid movement are parallel to those of total length extension, except possibly in the case of septate cells. Furthermore, by calculating the growth rate of various portions of the cell surface, it appears likely that the limits of the site of cylindrical envelope assembly lie between the distal tips of the nucleoid; the old poles show zero growth rate. Coupling of nucleoid extension with increase of cell length is envisaged as occurring through an exponentially increasing number of DNA-surface attachment sites occupying most of the available surface.
Integrating Order Information and Event Relation for Script Event Prediction

There has been a recent line of work automatically learning scripts from unstructured texts, by modeling narrative event chains. While the dominant approach group events using event pair relations, LSTMs have been used to encode full chains of narrative events. The latter has the advantage of learning long-range temporal orders, yet the former is more adaptive to partial orders. We propose a neural model that leverages the advantages of both methods, by using LSTM hidden states as features for event pair modelling. A dynamic memory network is utilized to automatically induce weights on existing events for inferring a subsequent event. Standard evaluation shows that our method significantly outperforms both methods above, giving the best results reported so far.
Deoxyribonucleic Acid-dependent Ribonucleic Acid Polymerase Activity in Cells Infected with Influenza Virus

Deoxyribonucleic acid (DNA)-dependent ribonucleic acid (RNA) polymerase activity was assayed on nuclear preparations of chick embryo fibroblast cells at various times after infection with an influenza A virus (fowl plague virus) and was compared with the activity of uninfected cells. Polymerase activity was increased by about 60% by 2 hr after infection, and this increase coincided with an increase in RNA synthesis in infected cells, as determined by pulse-labeling with uridine. No difference could be detected between the polymerases of infected and uninfected cells as to their requirements for DNA primer, divalent cations, and nucleoside triphosphates, and they were equally sensitive to addition of actinomycin D to the reaction mixture. It is possible that host cell DNA-dependent RNA polymerase is involved in the replication of influenza virus RNA.
Clinical Presentation and Severity of Viral Community-Acquired Pneumonia in Young Nepalese Children

Background: Most deaths from pneumonia in children <5 years of age occur in developing countries, where information about the clinical impact and severity of viral causes of respiratory infections is limited. Methods: From June 29, 2004 to June 30, 2007 we evaluated 2230 cases of pneumonia (World Health Organization criteria) in children aged 2 to 35 months in Bhaktapur, Nepal. A nasopharyngeal aspirate from each case was examined for 7 respiratory viruses using reverse-transcription polymerase chain reaction. We compared illness duration, severity, and treatment failure between cases positive and negative for the individual viruses in multiple regression models. Results: A total of 2219 cases had a valid polymerase chain reaction result and were included in the analyses. Overall, 46.1% of cases were 2 to 11 months of age. Being infected with respiratory syncytial virus (RSV) was associated with lower chest indrawing (odds ratio [OR] 2.17; 95% confidence interval [CI] 1.42–3.30) and, among infants, oxygen saturation <93% (OR: 1.88; CI: 1.32–2.69). Among the 2088 nonsevere pneumonia cases, those positive for RSV had a longer time to recovery (hazard ratio 0.82; CI 0.75–0.90; P < 0.001) and an increased risk of treatment failure (OR: 1.75; CI: 1.34–2.28; P < 0.001) than the RSV negative cases. Conclusions: Being infected with RSV was associated with a more severe clinical presentation of pneumonia, longer illness duration, and increased risk of treatment failure. The severity of RSV infection was age related, infants being more severely affected.
An Efficient Double-Filter Hardware Architecture for H.264/AVC Deblocking Filtering

In this paper, a novel hardware architecture for real-time implementation of the adaptive deblocking filtering process specified by the H.264/AVC video coding standard, is presented. The deblocking filter is a computationally and data intensive tool resulting in an increased execution time of both the encoding and decoding processes. The proposed architecture is based on a double- filter strategy that results in a significant saving in filtering cycles, memory requirements and gate count when compared with state-of-the-art approaches. The proposed architecture is implemented in synthesizable HDL at RTL level and verified with the reference software. This hardware is designed to be used as part of a complete H.264/A VC video coding system.
Optimization and In Vivo Evaluation of an Oral Dual Controlled-Release Tablet Dosage Form of Insulin and Duck Ovomucoid

The objectives of the present study were to (1) optimize the release rate of insulin from compressed microparticulates and (2) compare the in vivo hypoglycemic effect of optimized insulin microparticulates with compressed enzyme inhibitor (duck ovomucoid) and without inhibitor. A 3-factor, 15-run Box Behnken design was used to construct polynomial models correlating the dependent and independent variables. Independent processing variables were rate of addition of the alcoholic Eudragit© L100 dispersion, volume of the antisolvent, and compression pressure. Responses were cumulative percent of insulin released from 1–6 hours. Insulin and ovomucoid release was simultaneously analyzed by high-performance liquid chromatography. They demonstrated variable release rates, which were optimized to the Higuchi's square root of time model to release the insulin and the inhibitor over 6 hours. The relationship between dissolution profiles and process parameters were demonstrated by contour and response surface plots. In vivo hypoglycemic effect was evaluated in rabbits in a 3-way crossover design. Cocompressed microparticulates of insulin and duck ovomucoid displayed a 3.2-fold greater hypoglycemic effect when compared with a similar preparation without ovomucoid. This study demonstrated the potential benefits of dosage forms with dual controlled-release mechanisms for both the protein and enzyme inhibitor.
Development of a flocculation sub-model for a 3-D CFD model based on rectangular settling tanks.

To assess performance and evaluate alternatives to improve the efficiency of rectangular Gould II type final settling tanks (FSTs), New York City Department of Environmental Protection and City College of NY developed a 3D computer model depicting the actual structural configuration of the tanks and the current and proposed hydraulic and solids loading rates. Fluent 6.3. 26™ was the base platform for the computational fluid dynamics (CFD) model, for which sub-models of the SS settling characteristics, turbulence, flocculation and rheology were incorporated. This was supplemented by field and bench scale experiments to quantify the coefficients integral to the sub-models. The 3D model developed can be used to consider different baffle arrangements, sludge withdrawal mechanisms and loading alternatives to the FSTs. Flocculation in the front half of the rectangular tank especially in the region before and after the inlet baffle is one of the vital parameters that influences the capture efficiency of SS. Flocculation could be further improved by capturing medium and small size particles by creating an additional zone with an in-tank baffle. This was one of the methods that was adopted in optimizing the performance of the tank where the CCNY 3D CFD model was used to locate the in-tank baffle position. This paper describes the development of the flocculation sub-model and the relationship of the flocculation coefficients in the known Parker equation to the initial mixed liquor suspended solids (MLSS) concentration X0. A new modified equation is proposed removing the dependency of the breakup coefficient to the initial value of X0 based on preliminary data using normal and low concentration mixed liquor suspended solids values in flocculation experiments performed.
Cholecystokinin modulation of maternal behavior

behavior is regulated by several neurotransmitters, neuropeptides, and hormones. This mini-review focuses on the role of cholecystokinin (CCK), a neuropeptide and gut hormone best known as a satiety signal, in mediating maternal behavior. In addition to the role of CCK in the infant in mother-infant interactions, maternal CCK appears to also be important. We discuss maternal behavior research, mainly in rats, that has examined the effect of administering CCK to dams, CCK-opioid interactions, and maternal behavior in rats that lack CCK1 receptors. We discuss the possibility that CCK might play a role in neurological adjustments during pregnancy that ultimately influence behavioral adaptations by the offspring during lactation. Finally, we hypothesize that maternal CCK is also involved in maternal memory and reward. Keywords: cck, maternal behavior, opioid, lactation, nutrition.
A Highly Reliable Cu Interconnect Technology for Memory Device

This paper describes the development of Cu interconnect technology for memory devices. A highly reliable sub 50 nm Cu interconnect lines were successfully fabricated by using optimized iPVD barrier/seed and electroplating process. The resistivity of Cu lines was reviewed with that of Al for extendibility of Cu. The Cu TDDB lifetime in user conditions was investigated to confirm the reliability of Cu process integration. It can be predicted that Cu metallization can satisfy the requirements of sub 50 nm trench pattern, which are lower resistance than Al and good reliabilities.
Identification of transactivation-response sequences in the long terminal repeat of bovine immunodeficiency-like virus

Transient expression assays using the reporter gene that encodes chloramphenicol acetyltransferase were used to identify cis-acting sequences necessary for bovine immunodeficiency-like virus (BIV) transactivation. Computer analyses identified two RNA stem-loop structures located immediately downstream of the transcription start site in the long terminal repeat. Deletion analysis of the long terminal repeat indicated that sequences containing the proximal stem-loop structure located between +4 and +31 are required for virus-specific transactivation. Therefore, BIV likely utilizes a mechanism of transactivation similar to that of the human and simian lentiviruses.
Probabilistic Structure from Sound

Auditory perception is one of the most important functions for robotics applications. Microphone arrays are widely used for auditory perception in which the spatial structure of microphones is usually known. In practice, microphone array calibration can be tedious and other devices or means are required. The structure from sound (SFS) approach addresses the problem of simultaneously localizing a set of microphones and a set of acoustic events that provides a great flexibility to calibrate different setups of microphone arrays. However, the existing method does not take measurement uncertainty into account and does not provide uncertainty estimates of the SFS results. In this paper, we propose a probabilistic structure from sound (PSFS) approach using the unscented transform in which the uncertainties of the PSFS results are also available. In addition, a probabilistic sound source localization approach using the PSFS results is provided to improve sound source localization accuracy. The ample results of simulation and experiments using low-cost, off-the-shelf microphones demonstrate the feasibility and performance of the proposed PSFS approach.
Impact of IgM and IgG3 Anti-HLA Alloantibodies in Primary Renal Allograft Recipients

Background With standard IgG donor-specific anti-HLA antibody (DSA) testing, it is unclear which immunoglobulin-G (IgG) DSA positive patients will fail. We looked further into the immune response by studying immunoglobulin-M (IgM) and IgG subclass 3 (IgG3) DSA to determine if these identify the IgG DSA patients at highest risk for allograft loss. Methods In 189 consecutively transplanted primary renal allograft recipients, sera were collected sequentially pre- and posttransplant. Of the 189, 179 patients had sera available to retrospectively test for anti-HLA IgG, IgM, and IgG3 antibodies via LABScreen single-antigen bead assay and were included in the study. All patients had a negative crossmatch. Per patient, all DSA (IgM, IgG3, and IgG) refers to the same serologic specificity. Results Overall, 100 (56%) patients developed an alloimmune response (IgM or IgG DSA positive, or both). Ninety-five patients developed IgM DSA and 47 patients developed IgG DSA. IgM DSA was detected in 42 of 47 patients with IgG DSA. IgM DSA alone did not increase the allograft loss risk, whereas IgG DSA did (P=0.002). Once IgG DSA appeared, IgM DSA persisted in 33 patients and an isotype switch to IgG3 positive DSA occurred in 25 patients. Patients with IgM persistent IgG3 positive DSA (n=19) were more likely to have allograft failure than those without (P=0.02). Conclusion This study shows the evolution of the humoral immune response from IgM to IgG DSA posttransplant. We found that development of IgM persistent IgG3 positive DSA identifies the most dangerous IgG DSA subpopulation.
Prostaglandins Inhibit 5-Lipoxygenase-Activating Protein Expression and Leukotriene B4 Production from Dendritic Cells Via an IL-10-Dependent Mechanism1

PGs produced from arachidonic acid by the action of cyclooxygenase enzymes play a pivotal role in the regulation of both inflammatory and immune responses. Because leukotriene B4 (LTB4), a product of 5-lipoxygenase (5-LO) pathway, can exert numerous immunoregulatory and proinflammatory activities, we examined the effects of PGs on LTB4 release from dendritic cells (DC) and from peritoneal macrophages. In concentration-dependent manner, PGE1 and PGE2 inhibited the production of LTB4 from DC, but not from peritoneal macrophage, with an IC50 of 0.04 μM. The same effect was observed with MK-886, a 5-LO-activating protein (FLAP)-specific inhibitor. The decreased release of LTB4 was associated with an enhanced level of IL-10. Furthermore, the inhibition of LTB4 synthesis by PGs was significantly reversed by anti-IL-10, suggesting the involvement of an IL-10-dependent mechanism. Hence, we examined the effects of exogenous IL-10 on the 5-LO pathway. We demonstrate that IL-10 suppresses the production of LTB4 from DC by inhibiting FLAP protein expression without any effect on 5-LO and cytosolic phospholipase A2. Taken together, our results suggest links between DC cyclooxygenase and 5-LO pathways during the inflammatory response, and FLAP is a key target for the PG-induced IL-10-suppressive effects.
Structure and expression of the mouse myelin proteolipid protein gene

The gene for the mouse myelin proteolipid protein has been isolated and the seven exons have been sequenced. Since the sequence of a rat proteolipid protein cDNA and partial sequence of the human proteolipid protein gene have been determined, it was possible to demonstrate a very high degree of conservation for the protelipid protein gene exons among species. While there are some nucleotide changes, the protein coding region of the mouse gene encodes protein that is totally conserved relative to both rat and human prteolipid proteins. The regulatory and noncoding regions of the proteolipid protein gene are also highly conserved. The upstream regulatory and 5′‐noncoding region of the gene is 92% homologous to the comparable region of the human proteolipid protein gene, and the 3′‐noncoding region of the mouse gene is approximately 90% homologous to a rat proteolipid protein cDNA through 2,200 nucleotides of 3′‐noncoding DNA.S1 nuclease protection experiments indicated that the major 5′‐end for proteolipid protein mRNAs from mouse, rat human, ro baboon is approximately 147–160 nucleotides upstream from the initial methionine codon of the protein coding region. Other S1 nuclease protection experiments indicated the possible existence of an alernative splice site within exon 3, which may produce mRNA for DM20. This mRNA is approximately 100 nucleotides shorter than that for the protelipid protein, and it is missing the latter half of exon 3, that is, amino acids 116–150 of the proteolipid protein sequence.
Chronic alcoholism causes deleterious conditioning of innate immunity.

AIMS To examine the immune consequences of chronic alcoholism in man, in relation to the known association between alcoholism and raised incidence and severity of infections. METHODS In 36 alcoholics without liver disease, at the point of commencing withdrawal from alcohol, the following measures of immune competence were measured: the immunophenotypes of cells, acute phase proteins, the endotoxin-neutralizing capacity (ENC) of the serum, titers of anti-lipopolysaccharide (LPS) antibodies, and ex vivo cytokine inducibility in T cells and monocytes (TNFalpha, IL1beta, IL1RA, IL4, IL6, IL8, IL10 and IL12). The results were compared to those from healthy volunteers (day controls). Measures were repeated after 8-13 days of abstinence. RESULTS LPS-binding protein (LBP) and soluble CD14 (sCD14) were significantly increased in patients' sera at the outset of withdrawal, whereas reduced titers of anti-LPS IgG (P = 0.012) and a reduced ENC (P = 0.001) were measured. Only ENC rapidly returned to normal values after withdrawal therapy. Cytokine induction with phorbol ester showed no significant alterations in patients' T cells. Patients' monocytes, however, responded to LPS stimulation with enhanced IL1beta-, but reduced TNFalpha- and IL12-production (P = 0.004, P = 0.0042 and P = 0.001, respectively). While IL1- and TNFalpha-responses normalized after the withdrawal period, impairment of the IL12 response persisted throughout the observation period of 2 weeks. CONCLUSIONS Alcoholism results in a prolonged LPS-mediated hypoinflammatory conditioning of the innate but not the adaptive immune system, which is not reversed immediately after withdrawal. This alcohol-induced status of the immune system predisposes to infections and sepsis by blunting initial response to the pathogens.
High-dose Thiotepa as Consolidation Therapy With Autologous Hematopoietic Stem Cell Transplantation for High-risk Ewing Family Tumors: Single-institution Experience

High-dose therapy (HDTx) with autologous stem cell rescue has been widely applied in very–poor-risk pediatric solid tumors. Promising data have become available with the use of high-dose busulfan, whereas high-dose (HD) thiotepa is less commonly used. We report retrospectively our single-institution experience from 1986 to 2012 of single and tandem HDTx with special emphasis on HD-thiotepa as the backbone of HD regimen in Ewing family tumors, including all 24 patients in the Helsinki University Hospital referral area in population-based fashion (Ewing sarcoma 9, Askin tumor 9, peripheral neuroectodermal tumor 6). The 10-year overall survival for the entire cohort was 0.73±0.01. Thirteen out of the 24 underwent HDTx (10 single, 3 tandem). The HDTx regimen consisted of HD-thiotepa (900 mg/m2), VP16, and carboplatin. Additional HD-melphalan and total body irradiation were used in the tandem regimens. There was no toxic mortality. The 5-year event-free survival was 0.73±0.16 for high-risk cases transplanted in 1CR. In the relapse group, 1 out of the 3 survived. Radiotherapy to axial sites was given safely in combination with HD-thiotepa in all 3 patients. Thiotepa-based HDTx approach resulted in an encouraging outcome without toxic mortality for high-risk patients. HD-thiotepa merits further studies in larger controlled series.
Ten-year follow-up of behavioral, family-based treatment for obese children.

Using a prospective, randomized, controlled design, we examined the effects of behavioral family-based treatment on percent overweight and growth over 10 years in obese 6- to 12-year-old children. Obese children and their parents were randomized to three groups that were provided similar diet, exercise, and behavior management training but differed in the reinforcement for weight loss and behavior change. The child and parent group reinforced parent and child behavior change and weight loss, the child group reinforced child behavior change and weight loss, and the nonspecific control group reinforced families for attendance. Children in the child and parent group showed significantly greater decreases in percent overweight after 5 and 10 years (-11.2% and -7.5%, respectively) than children in the nonspecific control group (+ 7.9% and + 14.3%, respectively). Children in the child group showed increases in percent overweight after 5 and 10 years (+ 2.7% and + 4.5%, respectively) that were midway between those for the child and parent and nonspecific groups and not significantly different from either. At 10 years, child height was related strongly to the height of the parent of the same sex (r = . 78 children were 1.8 cm taller than their parents, with no differences in height between groups.
Three Different Ways Mental Health Nurses Develop Quality Therapeutic Relationships

The purpose of this study was to determine if there were different ways in which mental health nurses develop quality therapeutic relationships with patients. A taxonomy of 140 attributes were identified as important to the formation of a quality therapeutic relationship in mental health nursing. These attributes provided the basis for the development of a Q-sort instrument, which was piloted. Results led to the identification of three clusters of mental health nurses who share similar beliefs regarding the attributes required to develop a quality therapeutic relationship with patients. These groupings of attributes were called “Equal Partner,” “Senior Partner,” and “Protective Partner. ” Recommendations are provided and include that nurses consider their nursing style in their choice of employment environment and that managers consider their nurses' individual styles in determination of an optimal case mix.