Miracle-dz/UniFAR-FTUs huggingface dataset:
Two‐dimensional gel‐based proteomic of the caries causative bacterium Streptococcus mutans UA159 and insight into the inhibitory effect of carolacton

Streptococcus mutans is considered to be the most cariogenic organism. Carolacton, isolated from the myxobacterium Sorangium cellulosum, shows the ability to disturb S. mutans biofilm viability that makes it a potential anti‐biofilm drug. However, the molecular mechanism of carolacton remains to be elucidated. In order to use proteomics to characterize the effect of carolacton, we constructed a 2DE‐based proteome reference map of the cytoplasmic and extracellular proteins for S. mutans in the present study. In total, 239 protein spots representing 192 different cytoplasmic proteins were identified by MALDI‐TOF MS and PMF. This represents the highest number of identified proteins so far for S. mutans UA159 in the pI range of 4–7 and would benefit further research on the physiology and pathogenicity of this strain. Based on the constructed reference map, the inhibitory effects of carolacton on S. mutans biofilm and planktonic‐growing cells were investigated. The results of the comparative proteome analysis indicate that carolacton exerts its inhibitory effects by disturbing the peptidoglycan biosynthesis and degradation and thereby causes damages to the integrity of the cell envelope, leading ultimately to cell death.
Changes in the Rheology and Microstructure of Ropy Yogurt During Shearing

Yogurt made with an exopolymer-producing (ropy) strain of Lactobacillus delbrueckii subsp. bulgaricus and non-ropy strain of Streptococcus thermophilus was subjected to an increasing shear rate. Samples taken at eight different shear rates were examined by scanning electron microscopy. SEM micrographs and shear stress curves were used to determine a «bond-strength» of the EPS/lactobacilli interaction. After the interaction was disrupted, the EPS was still incorporated with the casein, where it continued to influence viscosity
The substructure of ciliary microtubules.

Gill cilia from the freshwater mussel Elliptio complanatus were examined after negative staining with phosphotungstic acid. The doublet and central pair microtubules typically collapse on the grid supporting film so that the protofilaments making up the wall of each tubule spread into a visible array. Thirteen protofilaments can be seen to form both the central pair microtubules and subfibre A of each doublet. Subfibre B of the doublet consists of 10 protofilaments. As viewed in both normal and thiourea-treated cross-sectioned cilia, subfibre A appears as a complete microtubule with a circular profile and 26 nm diameter. Subfibre B is an incomplete, elliptically profiled tubule that shares, as a common wall or partition, 4 or 5 protofilaments of the A subfibre. The organization of the 3.5-nm thick protofilaments within the microtubules and their relationship to the various doublet appendages is discussed.
I / O Efficient Implementation of MapReduce CIS 5930

MapReduce is a programming model and an associated implementation used by Google for processing their massive data sets. It has a simple yet powerful interface that is amenable to a broad variety of problems. Since 2003, when the MapReduce framework was first created, more than ten thousand distinct programs have been implemented under this model. A large number of MapReduce tasks are now running on Googles clusters at any minute, processing huge amounts of data and gathering lots of useful information. For instance, in the single month of September 2007, more than 2 million MapReduce jobs have been completed, processing over 400,000 TB of input data [2]. The success of MapReduce stems from the fact that it is very easy for the programmer to write a simple program and run it effi-ciently on a thousand machines, greatly improving the engineers productivity. In this project, (since we dont have a thousand machines,) we will study the problem of how to implement the MapReduce interface efficiently on a single machine. Since the data size could be much larger than memory, I/O-efficient techniques that you have learned from class will be useful (and required! ).
Lexically-based learning and early grammatical development

Pine & Lieven (1993) suggest that a lexically-based positional analysis can account for the structure of a considerable proportion of children's early multiword corpora. The present study tests this claim on a second, larger sample of eleven children aged between 1;0 and 3;0 from a different social background, and extends the analysis to later in development. Results indicate that the positional analysis can account for a mean of 60% of all the children's multiword utterances and that the great majority of all other utterances are defined as frozen by the analysis. Alternative explanations of the data based on hypothesizing underlying syntactic or semantic relations are investigated through analyses of pronoun case marking and of verbs with prototypical agent–patient roles. Neither supports the view that the children's utterances are being produced on the basis of general underlying rules and categories. The implications of widespread distributional learning in early language development are discussed.
Understanding Mentorship in a Research Training Program for Point-of-Care Clinicians

Evidence-based practice (EBP) is essential to high-quality patient care and can contribute to healthcare cost savings, yet nurses and other clinicians at the point of care report barriers to engagement with research and translating it to the clinical setting. Mentorship has been shown to improve nurses’ understanding and implementation of EBP. In this article, we describe a mentorship model in a successful program to support point-of-care nurses in conducting small-scale research projects, many of which have led to practice changes and/or cost savings.
Incidence of Genital Warts in Adolescents and Young Adults in an Integrated Health Care Delivery System in the United States Before Human Papillomavirus Vaccine Recommendations

Background Information on genital wart incidence in adolescents and young adults before human papillomavirus (HPV) vaccination is important for understanding the impact of the vaccine on the epidemiology of this early outcome of HPV infection. Methods The study population included 11- to 29-year-old enrollees of Northern California Kaiser Permanente between July 1, 2000, and July 1, 2005, before the availability of the HPV vaccine. We identified genital warts with an algorithm combining genital wart–specific International Classification of Diseases, Ninth Revision, Clinical Modification codes (078.10, 078.11, and 078.19) with physician-recorded anatomic locations. We calculated sex- and age-specific incidence rates of genital warts and described the specific anatomic location of presentation, as well as recurrences of genital warts. Results We identified 1,682 cases of genital warts among 181,264 individuals. The incidence rate was highest among women (6.3/1000 person-years) and men (2.9/1000 person-years) aged 20 to 24 years old. Among women (n = 96,792), 63.4% of the 1240 incident genital wart cases occurred on the vulva and 21.1% on the cervix. Among men (n = 84,472), 91.6% of the 442 incident genital wart cases did not have a specific anatomic location recorded. Most people with an incident genital wart diagnosis (87.2%) did not have a recurrence during the observation period. Conclusions Our study found that the incidence of genital warts was highest among persons aged 20 to 24 years using a unique method to identify the location of the wart. Information on incidence of genital warts before vaccine use provides baseline data that can be used to measure HPV vaccine impact.
HYDROGELS AS A DRUG DELIVERY SYSTEM AND APPLICATIONS: A REVIEW Review Article

Once used for simple encapsulation of cells or drugs, in homogenous materials, today’s hydrogels are more complex smart polymers with different types of ligands and cross links allowing for highly regulated structures and different bioresponsive functionalities. This review will emphasize on the various aspects of the hydrogels. Hydrogels that undergo swelling changes in response to specific biomolecules have become increasingly important because of their potential applications in the development of biomaterials and drug delivery systems and the biomedical applications of the hydrogels. We concentrate on the bioresponsive hydrogels and sensors, also introduces the physical background of the special properties of stimuli-responsive hydrogels; use of the various transducers describing changes in physical properties of the hydrogels. This paper considers the possibility of using artificial neural network models to identify model for swelling behavior as new techniques.
Assessment of a multimarker strategy for prediction of mortality in older heart failure patients: a cohort study

Objective Primarily to develop a multimarker score for prediction of 3-year mortality in older patients with decompensated heart failure (HF). Design Prospective cohort study. Setting Secondary care. Single centre. Patients and biomarkers 131 patients, aged ≥65 years, with decompensated HF were included. Assessment of biomarkers was performed at discharge. Primary outcome measure 3-year mortality. Results Mean age was 73±11 years; mean left ventricular ejection fraction , 43±14%; 53% were male. The 3-year mortality was 53.4%. The following N-terminal brain natriuretic peptide (NTproBNP) levels could optimally stratify mortality: <2000 ng/l (n=39), 30.8% mortality; 2000–8000 ng/l (n=58), 51.7% mortality; and >8000 ng/l (n=34), 82.4% mortality. However, in the 2000–8000 ng/l range, NTproBNP levels had low-prognostic capacity, based on the area under the receiver operating characteristic curve (AUC=0.53; 95% CI 0.40 to 0.67). In this group, multivariate analysis identified age, cystatin C (CysC), and troponin T (TnT) levels as independent risk factors. A risk score based on these three risk factors separated a high-risk and low-risk groups within the NTproBNP range of 2000–8000 ng/l. The score exhibited a significantly higher AUC (0.75; 95% CI 0.62 to 0.86) than NTproBNP alone (p=0.03) in this NTproBNP group and had similar prognostic capacity as NTproBNP in patients below or above this NTproBNP range (p=0.57). Net reclassification improvement and integrated discriminatory improvement in the group with NTproBNP levels between 2000 and 8000 ng/l was 54% and 23%, respectively, and in the whole cohort 22% and 11%, respectively. Conclusions Our results suggested that, to assess risk in HF, older patients required significantly higher levels of NTproBNP than younger patients. Furthermore, a risk score that included TnT and CysC at discharge, and age could improve risk stratification for mortality in older patients with HF in particular when NTproBNP was moderately elevated.
Endoscopic endonasal skull base approach for parasellar lesions: Initial experiences, results, efficacy, and complications

Background: Endoscopic surgery is suitable for the transsphenoidal approach; it is minimally invasive and provides a well-lit operative field. The endoscopic skull base approach through the large opening of the sphenoid sinus through both nostrils has extended the surgical indication for various skull base lesions. In this study, we describe the efficacy and complications associated with the endoscopic skull base approach for extra- or intradural parasellar lesions based on our experiences. Methods: Seventy-four cases were treated by an endoscopic skull base approach. The indications for these procedures included 55 anterior extended approaches, 10 clival approaches, and 9 cavernous approaches. The operations were performed through both the nostrils using a rigid endoscope. After tumor removal, the skull base was reconstructed by a multilayered method using a polyglactin acid (PGA) sheet. Results: Gross total resection was achieved in 82% of pituitary adenomas, 68.8% of meningiomas, and 60% of craniopharyngiomas in anterior extended approach and in 83.3% of chordomas in clival approach, but only in 50% of the tumors in cavernous approach. Tumor consistency, adhesion, and/or extension were significant limitations. Visual function improvements were achieved in 37 of 41 (90.2%) cases. Cerebrospinal fluid (CSF) leakage (9.5%), infections (5.4%), neural injuries (4.1%), and vascular injuries (2.7%) were the major complications. Conclusions: Our experiences show that the endoscopic skull base approach is a safe and effective procedure for various parasellar lesions. Selection of patients who are unlikely to develop complications seems to be an important factor for procedure efficacy and good outcome.
Characterization of an Alternative Chromatin Remodeling to Parasperm in a Cottid Fish, Hemilepidotus gilberti

The dimorphic sperm of Hemilepidotus gilberti, i.e., haploid eusperm and diploid parasperm, have different morphologies corresponding to their own roles in fertilization. To estimate how these specific sperm morphologies were established, we focused on the nuclear morphologies and examined their changing processes in dimorphic spermiogenesis. Electron microscopic observation revealed that, in euspermatids, chromatin condensation first appeared as a mosaic pattern of moderate electrodense material in the peripheral region of the round nucleus. Those materials spread across the whole area to form a uniformly condensed nucleus. Chromatin condensation began similarly in paraspermatids to that in euspermatids. These became localized to one side of a nucleus and further condensed to form strong electrodense chromatin clusters, which are a specific feature of parasperm. From the remodeled nuclei of eusperm and parasperm, we found five and three kinds of sperm-specific basic proteins (SBPs), respectively, substituted to histones. The N-terminus amino acid sequences of the SBPs suggest that, in parasperm, one major SBP and two minor ones were distinct from each other. In eusperm nuclei, two kinds of specific SBPs were detected in addition to the homologs of parasperm SBPs. The specific SBPs had homologous amino acid sequences with huge arginine clusters, and one of them was most dominant among the five kinds of SBPs. The different combinations of SBPs in the eusperm and parasperm may cause a specific pattern of chromatin condensation in the dimorphic sperm nuclei of H. gilberti.
GABAergic Transcallosal Neurons in Developing Rat Neocortex

In the mature cerebral cortex the interhemispheric connections across the corpus callosum appear to be essentially completely excitatory on the basis of both immunocytochemical and electrophysiological studies. During late embryonic development, however, immunocytochemical staining reveals numerous GABA‐positive fibres in the callosum, which later largely disappear. The origin of these fibres and whether they represent functional GABAergic neurons has not been established. In the present study we used a combination of retrograde labelling in vivo with electrophysiology and immnunocytochemistry in cell culture to show that transiently at birth in rat pups a substantial number of transcallosal cortical cells are functional GABAergic neurons. Possible roles and fates for these neurons are discussed.
[Comparison between manual acupuncture and electroacupuncture for hot flashes and sex hormone of perimenopausal syndrome].

OBJECTIVE To compare the effect and differences sex the influence of hormone levels of perimenopau-sal syndrome patients between manual acupuncture and electroacupuncture (EA). METHODS A total of 50 cases with perimenopausal syndrome were randomly assigned into an manual acupuncture group (27 cases) and an EA group (23 cases), and 1 case dropped in the EA group. The acupoints in the two groups were Guanyuan (CV 4), Zigong (EX-CA 1), Tianshu (ST 25), and Sanyinjiao (SP 6). Acupuncture with 3-time small and even manipulation of lifting, thrusting and twirling was used in the acupuncture group, once 10 min. EA with sparse-dense wave and 10 Hz/50 Hz was applied in the EA group for 30 min. The treatments in the two groups were for continuous 8 weeks (24 times in total), once the other day, 3 times a week. The scores of 24-hour hot flashes even, menopausal rating scale (MRS) and menopause-specific quality of life questionnaire (MENQOL) were recorded before treatment and after 4-week and 8-week treatment, as well as 12 and 24 weeks after treatment. Serum sex hormone levels were tested before and after 8-week treatment as well as 12 weeks after treatment, including serum follicle-stimulating hormone (FSH), luteinizing hormone (LH), and estracliol (E2). RESULTS Compared with those before treatment, the 24-hour hot flashes even score, MRS and MENQOL scores were significantly lower after 4-week and 8-week treatments, 12 and 24 weeks after treatment (all P<0.05). All the above scores after 8-week treatment were lower than those after 4-week treatment (all P<0.05); and the scores 12 and 24 weeks after treatment were lower than those after 4-week and 8-week treatments (all P<0.05); all the scores after treatment were not significantly different at any time between the two groups (all P>0.05). Compared with those before treatment, serum FSH and E2 apparently improved in the two groups after 8-week treatment and 12 weeks after treatment (all P<0.05). LH levels did not significantly change in the two groups (all P>0.05). All the serum sex hormone levels showed no significant difference between the two groups (all P>0.05). CONCLUSIONS Both acupuncture and EA can improve perimenopausal symptoms and serum sex hormone. The effects are similar.
Oxidative Stress-induced Peptidoglycan Deacetylase in Helicobacter pylori*

Structural modification of peptidoglycan (PG) is one of the mechanisms that pathogenic bacteria use to evade the host innate immune system. For the noninvasive human gastric pathogen Helicobacter pylori, PG delivery to the host cells is one trigger of the immune response. H. pylori HP310 was markedly up-expressed upon cell exposure to oxidative stress. However, disruption of HP310 did not produce a phenotype distinguishable from the parent, including oxidative stress resistance characteristics. HP310 shows very weak homology to a known gene pgdA encoding PG deacetylase in Streptococcous pneumoniae. PGs from wild type H. pylori and the HP310 mutant were purified and analyzed by matrix-assisted laser desorption ionization time-of-flight and high pressure liquid chromatography. The parent strain PG is partially deacetylated, whereas several major PG-deacetylated muropeptides are absent or significantly reduced in the HP310 mutant. PG deacetylase activity was directly demonstrated by use of pure PG and HP310 protein by measuring the release of acetic acid. The Gram-negative bacterium H. pylori is highly resistant to lysozyme (up to 50 mg/ml), but the HP310 mutant is less resistant to lysozyme compared with the parent strain. Complementation of an hp310 strain with the wild type gene restored lysozyme resistance. The purified PG from the mutant is more susceptible to lysozyme (0.3 mg/ml) digestion than the wild type PG. The PG deacetylation appears to confer lysozyme resistance to escape immune detection. HP310 is representative of a new subfamily of bacterial PG deacetylases.
Adaptive Optimal Control Without Weight Transport

Many neural control systems are at least roughly optimized, but how is optimal control learned? There are algorithms for this purpose, but in their current forms, they are not suited for biological neural networks because they rely on a type of communication that is not available in the brain, namely, weight transport—transmitting the strengths, or “weights,” of individual synapses to other synapses and neurons. Here we show how optimal control can be learned without weight transport. Our method involves a set of simple mechanisms that can compensate for the absence of weight transport in the brain and so may be useful for neural computation generally.
Pre-ablation magnetic resonance imaging of the cavotricuspid isthmus.

AIMS In this prospective pilot study, pre-procedural MRI was performed on patients undergoing radiofrequency ablation of the cavotricuspid isthmus (CTI) to assess variation in isthmus anatomy and its impact on catheter ablation. METHODS In 41 patients, 34 males, mean age 56 +/- 11.5 years, pre-procedural MRI was performed prior to ablation. On the basis of the magnetic resonance imaging (MRI), isthmus length and description of isthmus morphology was determined. Catheter ablation of the CTI was then performed using a standard technique by an experienced operator without prior knowledge of the MRI findings. RESULTS The following morphological variants of isthmus morphology were demonstrated: long isthmus, concave isthmus shape, simple pouches, and eccentric septally directed pouches distinct from the coronary sinus. There was a trend towards longer RF times for long and concave shaped CTI. Eccentric septally directed pouches were associated with significantly longer radiofrequency energy delivery times (29.5 +/- 24.5 min RF versus 14.5 +/- 12.9 min RF; P = 0.037). CONCLUSION The anatomy of the CTI is highly variable. Ablation difficulty can be predicted by the presence or absence of morphological variants and the length of CTI demonstrated by cardiac MRI.
An Integrated Approach to Functional Genomics: Construction of a Novel Reporter Gene Fusion Library for Sinorhizobium meliloti

ABSTRACT As a means of investigating gene function, we developed a robust transcription fusion reporter vector to measure gene expression in bacteria. The vector, pTH1522, was used to construct a random insert library for the Sinorhizobium meliloti genome. pTH1522 replicates in Escherichia coli and can be transferred to, but cannot replicate in, S. meliloti. Homologous recombination of the DNA fragments cloned in pTH1522 into the S. meliloti genome generates transcriptional fusions to either the reporter genes gfp+ and lacZ or gusA and rfp, depending on the orientation of the cloned fragment. Over 12,000 fusion junctions in 6,298 clones were identified by DNA sequence analysis, and the plasmid clones were recombined into S. meliloti. Reporter enzyme activities following growth of these recombinants in complex medium (LBmc) and in minimal medium with glucose or succinate as the sole carbon source allowed the identification of genes highly expressed under one or more growth condition and those expressed at very low to background levels. In addition to generating reporter gene fusions, the vector allows Flp recombinase-directed deletion formation and gene disruption, depending on the nature of the cloned fragment. We report the identification of genes essential for growth on complex medium as deduced from an inability to recover recombinants from pTH1522 clones that carried fragments internal to gene or operon transcripts. A database containing all the gene expression activities together with a web interface showing the precise locations of reporter fusion junctions has been constructed (www.sinorhizobium.org ).