Miracle-dz/UniFAR-FTUs huggingface dataset:
Two groups of bacteriophages infecting Streptococcus thermophilus can be distinguished on the basis of mode of packaging and genetic determinants for major structural proteins

A comparative study of 30 phages of Streptococcus thermophilus was performed based on DNA restriction profiles, DNA homology, structural proteins, packaging mechanisms, and host range data. All phages exhibited distinct DNA restriction profiles, with some phages displaying similarly sized restriction fragments. DNA homology was shown to be present among all 30 phages. The phages could be divided into two groups on the basis of their packaging mechanism as was derived from the appearance of submolar DNA fragments in restriction enzyme digests and the presence (cos-containing phages) or absence (pac-containing phages) of cohesive genomic extremities. Interestingly, the 19 identified cos-containing phages possessed two major structural proteins (32 and 26 kDa) in contrast to the remaining 11 pac-containing phages, which possessed three major structural proteins (41, 25, and 13 kDa). Southern hybridization demonstrated that all pac-containing phages tested contain homologs of the genes encoding the three major structural proteins of the pac-containing phage O1205, whereas all cos-containing phages tested exhibit homology to the gene specifying one of the structural components of the cos-containing phage phi 7201. Fifty-seven percent of the phages (both cos and pac containing) possessed the previously identified 2.2-kb EcoRI fragment of the temperate S. thermophilus phage Sfi18 (H. Brüssow, A. Probst, M. Frémont, and J. Sidoti, Virology 200:854-857, 1994). No obvious correlation was detected between grouping based on packaging mechanism and host range data obtained with 39 industrial S. thermophilus strains.
ABODE: Kernel home range estimation for ArcGIS, using VBA and ArcObjects

K Ke er rn ne el l H Ho om me e R Ra an ng ge e E Es st ti im ma at ti io on n f fo or r A Ar rc cG GI IS S, , u us si in ng g V VB BA A a an nd d A Ar rc cO Ob bj je ec ct ts s B By y P Pe et te e L La av ve er r 1 1 U Us se er r M Ma an nu ua al l ((B Be et ta a v v. .2 2-7 7 F Fe eb br ru ua ar ry y, , 2 20 00 05 5)) 5.1. Why we should look at them 30 5.2. How we should analyze them 31 6. Core Home Ranges 33 6.1. Does a core really exist? 33 6.2. How do we test for this? 33 7. Data driven and Biologically meaningful methods 36 8. Home range analysis is an important part of our study of animals and it is fraught with problems from data collection to final management implementation. ABODE is user-friendly freeware that can be used in ArcGIS to do both MCP and kernel analyses. Both batch and single processing are available, as well as automatic functions for asymptote analyses and core home range analyses. The code for this package is open, and can be manipulated to suit the needs of the user with minimal VBA and/or ArcObjects experience. The functionality in and the detailed documentation provided with ABODE are aimed to address some of the more contentious issues in home range analysis. Beyond providing documentation for ABODE, this 'user manual' is also aimed at giving the user background in home range theory and home range analyses. Should the user feel comfortable
Physical activity and survival after breast cancer diagnosis.

CONTEXT Physical activity has been shown to decrease the incidence of breast cancer, but the effect on recurrence or survival after a breast cancer diagnosis is not known. OBJECTIVE To determine whether physical activity among women with breast cancer decreases their risk of death from breast cancer compared with more sedentary women. DESIGN, SETTING, AND PARTICIPANTS Prospective observational study based on responses from 2987 female registered nurses in the Nurses' Health Study who were diagnosed with stage I, II, or III breast cancer between 1984 and 1998 and who were followed up until death or June 2002, whichever came first. MAIN OUTCOME MEASURE Breast cancer mortality risk according to physical activity category (<3, 3-8.9, 9-14.9, 15-23.9, or > or =24 metabolic equivalent task [MET] hours per week). RESULTS Compared with women who engaged in less than 3 MET-hours per week of physical activity, the adjusted relative risk (RR) of death from breast cancer was 0.80 (95% confidence interval [CI], 0.60-1.06) for 3 to 8.9 MET-hours per week; 0.50 (95% CI, 0.31-0.82) for 9 to 14.9 MET-hours per week; 0.56 (95% CI, 0.38-0.84) for 15 to 23.9 MET-hours per week; and 0.60 (95% CI, 0.40-0.89) for 24 or more MET-hours per week (P for trend = .004). Three MET-hours is equivalent to walking at average pace of 2 to 2.9 mph for 1 hour. The benefit of physical activity was particularly apparent among women with hormone-responsive tumors. The RR of breast cancer death for women with hormone-responsive tumors who engaged in 9 or more MET-hours per week of activity compared with women with hormone-responsive tumors who engaged in less than 9 MET-hours per week was 0.50 (95% CI, 0.34-0.74). Compared with women who engaged in less than 3 MET-hours per week of activity, the absolute unadjusted mortality risk reduction was 6% at 10 years for women who engaged in 9 or more MET-hours per week. CONCLUSIONS Physical activity after a breast cancer diagnosis may reduce the risk of death from this disease. The greatest benefit occurred in women who performed the equivalent of walking 3 to 5 hours per week at an average pace, with little evidence of a correlation between increased benefit and greater energy expenditure. Women with breast cancer who follow US physical activity recommendations may improve their survival.
NES-SOURCE: Indoor small-scale wireless control network protocol that has a communication failure point avoidance function

Wireless control network require delay guarantees and low packet error rates. The reason for communication delay and error is packet loss, and TDMA is used by many wireless control network technologies to avoid packet loss. However, TDMA protocols are difficult to implement. Besides, TDMA cannot avoid communication failure points due to changes in the environment caused by human intervention. We propose NES-SOURCE as a CSMA/CA based control network protocol. NES-SOURCE uses a source routing protocol, and if the NES-SOURCE node fails to communicate using primary route, the node avoid the communication failure point by to use secondary bypass route. NES-SOURCE is a low delay protocol. The reason is that NES-SOURCE can change the communication route at high speed. In addition, NES-SOUCE is implemented using a protocol stack that is compatible with IEEE 802.15. 4 g. We show that NES-SOURCE systems can be used for wireless control network systems, and in an environment where people moving are in and out, path change is more advantageous than retransmission from the point of view of the packet error rate.
Computer-aided radiation therapy simulation: image intensifier spatial distortion correction for large field of view digital fluoroscopy

An accurate method of correcting spatial distortion in digital fluoroscopy images has been developed for generating fluoroscopy-based large field of view images for computer-aided radiation therapy simulation. This method is applicable to arbitrary gantry rotations and arbitrary shifts of the image intensifier relative to the central axis of the x-ray beam. It is therefore suitable for conventional radiation therapy simulation techniques that involve the arbitrary positioning of the image intensifier by the operator. Spatial distortion is modelled as two image intensifier orientation-dependent components, the first resulting from the projection of the x-ray image onto the curved surface of the image intensifier front end, and the second produced by the image intensifier electron optics, interactions with external magnetic fields and the video system. A geometrical model approximates the first component. The second component is modelled by a third-order polynomial transformation. A weighted mean approach is employed to achieve accurate distortion correction when the image intensifier is oriented differently from the calibration orientations. Mean and maximum residual errors (measured in the plane of the isocentre) of 0.4 mm and 1.0 mm respectively have been achieved with just 48 calibration orientations in four dimensions (gantry rotation and lateral, longitudinal and vertical shifts of the image intensifier).
Plasmodium evasion of mosquito immunity and global malaria transmission: The lock-and-key theory

Significance Plasmodium falciparum malaria originated in Africa but became global as humans migrated around the world. It is now transmitted by many different anopheline mosquito species, but little is known about the adaptation of Plasmodium to different vectors. Here, we show that the mosquito immune system is a major barrier for some P. falciparum isolates to infect mosquitoes from a different continent. Pfs47 is a protein that makes parasites “invisible” to the mosquito immune system. We found that parasites expressing a Pfs47 haplotype compatible with a given vector species can evade mosquito immunity. These findings suggest that Pfs47-mediated evasion of the mosquito immunity was critical for malaria globalization and may be a key target to disrupt disease transmission. Plasmodium falciparum malaria originated in Africa and became global as humans migrated to other continents. During this journey, parasites encountered new mosquito species, some of them evolutionarily distant from African vectors. We have previously shown that the Pfs47 protein allows the parasite to evade the mosquito immune system of Anopheles gambiae mosquitoes. Here, we investigated the role of Pfs47-mediated immune evasion in the adaptation of P. falciparum to evolutionarily distant mosquito species. We found that P. falciparum isolates from Africa, Asia, or the Americas have low compatibility to malaria vectors from a different continent, an effect that is mediated by the mosquito immune system. We identified 42 different haplotypes of Pfs47 that have a strong geographic population structure and much lower haplotype diversity outside Africa. Replacement of the Pfs47 haplotypes in a P. falciparum isolate is sufficient to make it compatible to a different mosquito species. Those parasites that express a Pfs47 haplotype compatible with a given vector evade antiplasmodial immunity and survive. We propose that Pfs47-mediated immune evasion has been critical for the globalization of P. falciparum malaria as parasites adapted to new vector species. Our findings predict that this ongoing selective force by the mosquito immune system could influence the dispersal of Plasmodium genetic traits and point to Pfs47 as a potential target to block malaria transmission. A new model, the “lock-and-key theory” of P. falciparum globalization, is proposed, and its implications are discussed.
A pedestrian approach to ray shooting: shoot a ray, take a walk

We propose a very simple ray-shooting algorithm, whose only data structure is a triangulation. The query algorithm, after locating the triangle containing the origin of the ray, walks along the ray, advancing from one triangle to a neighboring one until the polygon boundary is reached. The key result of the paper is a Steiner triangulation of a simple polygon with the property that a ray can intersect at most O(log n) triangles before reaching the polygon boundary. We are able to compute such a triangulation in linear sequential time, or in O(log n) parallel time using O(n/log n) processors. This gives a simple, yet optimal, ray-shooting algorithm for a simple polygon. Using a well-known technique, we can extend our triangulation procedure to a multiconnected polygon with k components and n vertices, so that a ray intersects at most O(√κ log n) triangles. © 1995 Academic Press, Inc.
WRIP: logic restructuring techniques for wirelength-driven incremental placement

This paper presents WRIP - a Wirelength-driven Rewiring-based Incremental Placement which effectively reduces wirelength of the optimized placement of industrial large-scale standard cell designs. WRIP uses a powerful logic synthesis technique called logic rewiring which restructures the local circuits while preserving the logic functionality and reduces the wirelength under an accurate estimation of the half perimeter wirelength (HPWL) metric. We integrated WRIP into an industrial EDA tool and tested it upon several real designs with hundreds of thousands of movable objects. Tested on circuits which has been fully optimized by the state-of-the-art industrial placement tool, our experiments showed that on average WRIP reduces wirelength by 2.25% after placement and 2.45% after global routing in HPWL and Steiner WL model respectively. The runtime of WRIP is only about half an hour for the largest tested ASIC circuit. This is the first attempt to fully integrate powerful logic synthesis into industrial placement tools with real-life effectiveness and efficiency.
COMPARATIVE STUDY OF SPEECH RECOGNITION SYSTEM USING VARIOUS FEATURE EXTRACTION TECHNIQUES

It is very important to detect the speech endpoints accurately in speech recognition. This paper presents a comparative analysis of various feature extraction techniques of endpoint detection in speech recognition of isolated words in noisy environments. The endpoint detection problem is nontrivial for no stationary backgrounds where artifacts (i.e., no speech events) may be introduced by the speaker, the recording environment, and the transmission system. An optimum set of characteristics is identified by combining parameters from both time domain and frequency domain, in a robust approach for identification when the speech signal is corrupted by additive noise and channel distortion. The cases of colored noises such as babble noise, factory noise at different SNR values in conjunction with distortions due to recording medium were tested. Experimental results identify the optimal algorithm which significantly achieves the highest performance in the
Immunotoxin Complementation of HAART to Deplete Persisting HIV-Infected Cell Reservoirs

E.A. B. and I.P. are co-inventors on NIH-owned issued patents and patent applications for CD4-PE and 3B3-PE. This work was supported in part by the Intramural Program of the NIH (National Institute of Allergy and Infectious Diseases; National Cancer Institute), including the NIH Intramural AIDS Targeted Antiviral Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Different effects of ambulatory blood pressure monitoring on subjective and objective sleep quality

ObjectiveTo determine whether ambulatory blood pressure monitoring affects objective and subjective sleep quality in patients tested at home. MethodsSeventy consecutive patients (40 women and 30 men, aged 53±15 years), having ambulatory blood pressure monitoring to monitor the efficacy of antihypertensive treatment or to distinguish between hypertension or white-coat hypertension had an evaluation of their sleep quality on a first night with ambulatory blood pressure monitoring and the three following nights without ambulatory blood pressure monitoring. Ambulatory blood pressure monitoring was performed with an auscultatory device with a measure every 15 min during 24 h. Sleep evaluation criteria were both subjective (sleep quality score and sleep questionnaire) and objective (wrist actigraphy monitoring). Sleep parameters during night 1 with ambulatory blood pressure monitoring were compared with those during night 4 without ambulatory blood pressure monitoring. Usual quality of sleep of the patients was assessed by the mean sleep quality score over 7 consecutive days. ResultsThe sleep quality score was significantly higher for night 4 than for night 1 (7.3±2.1 vs. 5.3±2.3; P<0.0001). In contrast, actigraphy parameters (actual sleep time, mean activity score, and fragmentation index) were similar on night 1 and night 4 (6.7±1.2 vs. 6.9±1.2, 13.2±9.8 vs. 12.1±8.4, and 31.0±14.5 vs. 29.9±14.3, respectively). Subjective sleep quality was significantly altered by ambulatory blood pressure monitoring in good sleepers (mean sleep quality score ≥7, 73% of patients) but not in poor sleepers. The effect of ambulatory blood pressure monitoring on subjective sleep quality did not differ between dippers and nondippers. ConclusionsObjective sleep quality as assessed by wrist actigraphy is not significantly altered by ambulatory blood pressure monitoring, whereas subjective sleep quality is adversely affected in good sleepers.
An adaptive chaotic PSO for parameter optimization and feature extraction of LS-SVM based modelling

While training an LS-SVM model, two main challenges are parameter optimization and input feature extraction. The main purpose of this article is to address these two problems. Commonly used tools are PSO and BPSO, but they are not suitable for the optimization issues of many local optima owing to its random numbers used to update velocities. In this paper, an adaptive chaotic particle swarm optimization (cPSO) algorithm is proposed to enhance its global searching capability and local searching capability. The practicality of the proposed scheme is demonstrated by application to mineral process for the prediction models between production rate of the concentrated ore and the technical indexes. Compared with the original methods of grid search+PCA, GA+PCA, PSO+PCA as well as PSO+BPSO, the proposed strategy outperforms these existing methods in terms of convergence accuracy.
Improved Benefit of SPECT/CT Compared to SPECT Alone for the Accurate Localization of Endocrine and Neuroendocrine Tumors

Objective: To assess the clinical utility of SPECT/ CT in subjects with endocrine and neuroendocrine tumors compared to SPECT alone. Material and Methods: 48 subjects (31 women;17 men; mean age 54±11) with clinical suspicion or diagnosis of endocrine and neuroendocrine tumor had 50 SPECT/CT scans (32 Tc-99m MIBI, 5 post treatment I-131, 8 In-111 Pentetreotide, and 5 I-123 MIBG). SPECT alone findings were compared to SPECT/CT and to pathology or radiological follow up. Results: From the 32 Tc-99m MIBI scans, SPECT accurately localized the lesion in 22 positive subjects while SPECT/CT did in 31 subjects. Parathyroid lesions not seen on SPECT alone were smaller than 10 mm. In five post treatment I-131 scans, SPECT alone neither characterized, nor localized any lesions accurately. SPECT/CT revealed 3 benign etiologies, a metastatic lymph node, and one equivocal lesion. In 8 In-111 Pentetreotide scans, SPECT alone could not localize primary or metastatic lesions in 6 subjects all of which were localized with SPECT/CT. In five I-123 MIBG scans, SPECT alone could not detect a 1.1 cm adrenal lesion or correctly characterize normal physiologic adrenal uptake in consecutive scans of the same patient with prior history of adrenelectomy, all of which were correctly localized and characterized with SPECT/CT. Conclusion: SPECT/CT is superior to SPECT alone in the assessment of endocrine and neuroendocrine tumors. It is better in lesion localization and lesion characterization leading to a decrease in the number of equivocal findings. SPECT/CT should be included in the clinical work up of all patients with diagnosis or suspicion of endocrine and neuroendocrine tumors. Conflict of interest:None declared.
The diameter of the ileal J-pouch-anal anastomosis as an important risk factor of pouchitis – clinical observations

Summary Background Patients’ quality of life after restorative proctocolectomy depends on the potential complications. Stricture of the ileal pouch-anal anastomosis is one of the complications following restorative proctocolectomy. Material/Methods We analyzed the correlation between the diameter of the anastomosis and clinical parameters, including pouchitis disease activity index (PDAI), the activity of fecal M2-pyruvate kinase and maximum tolerable volume of the pouch. The study group consisted of 31 patients in whom covering ileostomy had been closed 72±50 months before enrolement to the study. Restorative proctocolectomy for ulcerative colitis or familial adenomatous polyposis coli had been performed in this group. Results The study did not show any correlation between the diameter of the anastomosis and primary indication for surgery, the time elapsed after restoration of the bowel continuity, the activity of fecal M2-pyruvate kinase, or maximum tolerable volume. However, meaningful correlations between the stricture of the anastomosis and the presence and activity of pouchitis, together with the ileal villi atrophy, were detected. Conclusions Stricture of the anastomosis appears to be an important factor increasing the incidence of pouchitis, and is independent of the underlying condition and time after the operation. Dilation of the anastomosis and prevention of stricture should constitute a permanent element of postoperative follow-up.
Recognition and Selfhood

At the end of the preceding study Mr. Katzaroff sketched one conception of recog­ nition that is almost identical to the one I reached myself following several experi­ ments on a hypnotic subject and a woman who was affected by Korsakoff Syndrome. I would like to add a few words on this theory of ''selfhood'' which both of us were led to, but which we expressed with more or less precision, and which is very similar to James' conception. Let us recall first of all that the psychological problem of recognition implies noth­ ing at all about the subject's consciousness of past events. For the logician, or the man in the street, or for the psychologist who regards mental activity from an external point of view, "recognition" doubtless means that the object one recognizes was already known at a previous time. But subjectively, is this consciousness of past occurrence, or more exactly of' 'once again,'' really contained in the most immediate experience of recognition, that is, in the subjective feeling of familiarity? It does not seem so: when we are shown a pattern which has been presented to us at a previous time, the impression of familiarity, knownness, similarity, emerges well before the awareness of its pre-existence, and may even stand alone. This is what introspection shows. It is true that in everyday life, we tend to attribute whatever we recognize to the past, and this can happen so rapidly that it seems integral to the immediate process of recognition. But this is merely an illusion. 1 If one considers the evolutionary origins of the psyche, one can clearly observe how recognition appears long before the ability to locate an experience in the past. In animals we can observe implicit recognition (of a certain prey, its gait, etc.) even when nothing in their behavior indicates that they have any conception of past time, nor any ability to date events. In the lives of children, the ability to recognize events appears long before any conception of the past. Furthermore, we have cases where a feeling of familiarity accompanies the percep­ tions of objects which the person is certain he has never had before: thus for instance
Radio-browsing for developmental monitoring in Uganda

We consider the extraction of information from broadcast radio speech in Uganda for the purposes of informing relief and development programmes by the United Nations. Although internet penetration in Uganda is low, mobile phones are ubiquitous and have made radio a vibrant medium for interactive public discussion. Vulnerable groups make use of radio to discuss issues related to, for example, agriculture, health, governance and gender by means of phone-in or text-in talk shows. We have compiled corpora and developed a radio-browsing system for Ugandan English and for two indigenous languages, Luganda and Acholi. The systems employ automatic speech recognisers using HMM/GMM, SGMM and DNN/HMM acoustic models as keyword spotters. We present the first results indicating promising performance of the radio-browsing system.