Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic effective size, Ne, tracks density in a small freshwater cyprinid, Pecos bluntnose shiner (Notropis simus pecosensis)

Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (NeV) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (NeD) for each sample. Estimates of Ne were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch‐per‐unit‐effort), NeV and NeD were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and NeV were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and NeD were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of Ne and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive‐bred and reared fish. The efficacy of Ne as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors.
Traffic specifications for the transmission of stored MPEG video on the Internet

Guarantees of quality-of-service (QoS) in the real-time transmission of stored video on the Internet is a challenging task for the success of many video on demand (VoD) applications. Two QoS classes have been specified by the IETF Integrated Services (intserv) Working Group: Guaranteed Services and Controlled-Load Services. For both of them, it is necessary to provide traffic sources with the capability of calculating the traffic characteristics to be declared to the network, Tspec, on the basis of a limited set of parameters statistically characterizing the traffic and the required level of QoS. The target of this paper is to develop an algorithm for the evaluation of the Tspec parameters which characterize the video stream when a given QoS is required. To this end an analytical framework modeling an MPEG stored-video server and the access network node is introduced. The video emission process is modeled with a switched batch Bernoulli process (SBBP), and performance in the video-server smoother is analytically evaluated. Then the token bucket at the network access point, loaded by the output traffic of the video-server smoother, is modeled to calculate the probability of marking nonconforming data packets.
GEOAIDA applied to SPOT satellite image interpretation

This paper investigates the application of a knowledge-based approach, founded on semantic networks, to the automatic land use mapping assisted by low resolution satellite images. Like the visual photo-interpretation, the automatic image interpretation considers scene and sensors knowledge, delivered by an expert photo-interpreter, as well as additional information about the region like the digital elevation model, the position of the emergent rocks, the mapping of the water bodies and the road-network. By this means, the analysis of a scene can be automatically performed, mimicking the reasoning of the photo-interpreter. The implementation of such proposal employed the GEOAIDA [J. Buckner et al., June 2001] system, a flexible environment for image interpretation developed at the University of Hanover, which exploits semantic networks to structure the domain specific knowledge. In the reported experiments, a multispectral SPOT 3 XS image was analysed resulting were evaluated and compared with a manually made reference map of the investigated scene. The automatically obtained results were evaluated and compared with a manually made reference map of the investigated scene. The experimental results demonstrate the potential of a knowledge-based approach for low resolution satellite images interpretation.
Analysis of Benzylisoquinoline-Type Alkaloids by Electrospray Tandem Mass Spectrometry and Atmospheric Pressure Photoionization

Benzylisoquinoline alkaloids found in the Papaveraceae family play a major role in pharmaceutical biology. This is the first systematic study dealing with electrospray tandem mass spectrometry (ESI-MS/MS) of all benzylisoquinolines found as biogenetic precursors of morphinan alkaloids. Tandem mass spectral data are presented for norlaudanosoline, laudanosoline, 4′-O-methyl-norlaudanosoline, 6-O-methyl-norlaudanosoline, norcoclaurine, coclaurine, N-methylcoclaurine, N-methyl-3′-hydroxycoclaurine, N-methyl-3′-O-methylcoclaurine, norreticuline and reticuline. This study compares results obtained using an ion trap mass spectrometer with those obtained using a triple quadrupole one. The results highlight the differences between the tandem-in-time versus the tandem-in-space principle, often hampering the development of ESI-MS/MS libraries. In addition, the use of the atmospheric pressure photoionisation technique for the analysis of such substances is discussed.
Than 1000 Loci An Enhanced Linkage Map of the Sheep Genome Comprising More

Access the most recent version at doi: 2001 11: 1275-1289; originally published online Jun 12, 2001; Genome Res. Medrano, Korena A. Paterson, Laurent Schibler, Roger T. Stone and Beryl van Hest Susan M. Galloway, Blair Harrison, Rachel J. Hawken, Stefan Hiendleder, Hannah M. Henry, Juan F. Heather R. Burkin, Judith E. Broom, Johannes Buitkamp, Lisa Cambridge, William T. Cushwa, Emily Gerard, Stephen S. Moore, Ken G. Dodds, Joanne M. Lumsden, Tracey C. van Stijn, Sin H. Phua, David L. Adelson, Bradley A. Freking, Ken J. Beh, Noelle E. Cockett, Nina Kang, Christopher D. Riffkin, Roger Drinkwater, Jillian F. Maddox, Kizanne P. Davies, Allan M. Crawford, Dennis J. Hulme, Daniel Vaiman, Edmond P. Cribiu, Than 1000 Loci An Enhanced Linkage Map of the Sheep Genome Comprising More
Microbiological Changes and Determination of Some Chemical Characteristics for Local Yemeni Cheese

The changes in microbiological parameters during the storage of local Yemeni cheese were studied. Both the smoked and the non smoked cheese were produced by using traditional techniques in some regions of Yemen. Microbiological examination was carried out at 2, 4 and 7 days of storage for serve cheese and compared with control cheese prepared in laboratory. During storage period, the total viable bacteria count, lactic acid bacteria, staphylococci, coliforms, yeast and molds increased and reached to 11.97, 10.36, 11.8, 13.4, 11.8 and 8.9 Log cfu/g, respectively, in some samples and then decreased at the end of storage period. Also, the number of coliforms, staphylococci, yeast and molds in cheese samples were higher than limits allowed by the national standards for Yemeni soft cheese. Pathogenic flora as Salmonella and Listeria were detected in some samples and disappeared at the end of storage period. The hygienic quality of smoked cheese was best than non smoked cheese. At the final days of storage a sharp drop in pH values changing from 5.4 to 4.1 was noticed. The average contents of chemical composition of smoked and non-smoked cheeses were that, moisture 46.55 and 57.27%, fat 21.29 and 20.67 %, protein 14.87 and 16.98% salt 5.01 and 3.75 % respectively.
Estimating dose‐response relationship between ethanol and risk of cancer using regression spline models

Cancers of the upper aero‐digestive tract (i.e., oral cavity, pharynx, larynx and oesophagus) are largely attributable to smoking and drinking habits, but the correct estimation of the dose‐response relationship between alcohol and cancer risk is challenging. Step functions are widely used to estimate risks and to evaluate trends of continuous exposure. However, results are influenced by the selection of the reference category and cutpoints. More flexible models, like spline regression and fractional polynomial models, may be an attractive alternative for avoiding strict assumptions about the dose‐response relationship. Data from a large series of hospital‐based case‐control studies conducted in Italy and the Swiss Canton of Vaud in the last 2 decades were reassessed to compare findings from logistic regression spline models and standard step function analysis. For all examined cancers, the risk increased to the consumption of 150 grams of ethanol per day (1.5 litre/day of wine), with a possible threshold effect emerging for cancer of the pharynx and larynx (<50 grams of ethanol per day) only. For higher consumptions, the risks flattened. Our study suggests that regression spline models can be useful to estimate the pattern of risk of a continuous exposure variable, such as alcohol consumption, and provide more accurate estimates than categorical analysis when ORs within each interval, especially in the reference category, are not homogeneous. © 2004 Wiley‐Liss, Inc.
Sentiment classification of customer reviews on electric products

A lot of terms represent the speaker's evaluation of the item. This evaluative character of the word is called its semantic orientation. The word with positive semantic orientation implies that the item is desirable, and on the other hand, the word with negative semantic orientation implies that the item is not desirable. We propose a method to estimate the semantic orientation(positive or negative) of Japanese products reviews, in which a pair of noun and adjective are selected as the corpus to determine the semantic orientation of the reviews and the semantic orientation scores of the review are calculated according to the corpus. The words which change the semantic orientation of a word called as "contextual valence shifter" such as "not", "very" "quite" are considered in the algorithm to determine the semantic orientation. In order to empirically evaluate the performance of the classification method for Japanese documents, 1400 reviews of two electric products, LCD and MP3 music player, are classified to two categories (positive or negative).
Spatial Distribution of Dialysate in Patients and its Implications to Intradialysate Diffusion

Objective To visualize and quantify the spatial distribution of dialysate in patients on continuous ambulatory peritoneal dialysis (CAPD) and, hence, estimate diffusion times for fluid “pockets” wherever intradialysate concentration gradients may not be dissipated by convective currents. Design Contrast medium was added to the dialysate of three supine CAPD patients before an exchange prior to computed tomographic (CT) scanning. Spatial information in the CT scanner was then downloaded to other computers and processed to produce impressive three-dimensional models of dialysate distribution using “wire frame technology. ” Results Models differed between patients but all demonstrated pooling of dialysate in the paracolic gutters, subphrenic space, and, especially, in the pelvic cavity. Some pockets of fluid were almost isolated. Quantitatively, the models can account for over 80% of the volume of the exchange (2.5 L), displaying an effective area of contact of 913 – 1450 cm2 between parietal peritoneum and dialysate. This amounts to only 11% – 21% of the anatomic area, again emphasizing the uneven distribution of dialysate. Ignoring very thin (< 0.1 mm) films of dialysate, the bulk (80%) had mean thicknesses ranging from 1.6 to 1.9 cm. Transcendental equations for bulk diffusion were then applied to these findings to determine a theoretical time for urea of about 2 – 3 hours to half-saturation, or 5 – 7 hours to 80% saturation, in the absence of convective currents. Conclusions The distribution of dialysate within the peritoneal cavity is very uneven, resulting in long diffusion times in fluid pockets wherever convective currents may be minimal. Hence, intradialysate diffusion should not be ignored when modeling peritoneal dialysis.
Can outpatient pharmacy data identify persons with undiagnosed COPD?

OBJECTIVE To develop and validate a method for identifying persons with undiagnosed chronic obstructive pulmonary disease (COPD) using outpatient pharmacy data. STUDY DESIGN Case-control analysis of managed care administrative data with clinical validation by spirometry and standardized questionnaires. METHODS Patients with a new diagnosis of COPD were matched to 3 control subjects by age and sex. Outpatient pharmacy utilization for the 2 years prior to the initial diagnosis was captured. Drugs associated with an eventual diagnosis of COPD were identified using conditional logistic regression, and then entered into a predictive algorithm using discriminant function analysis. The algorithm was tested in a second population from the same health plan and externally validated using 2 large multicenter databases. This system was clinically validated by testing 100 individuals identified by the algorithm with spirometry plus health status and respiratory symptoms questionnaires. RESULTS COPD patients used significantly more antibiotics, cardiac medications, and respiratory drugs than their matched controls. The final algorithm identified COPD patients with a sensitivity of 60% and specificity of 70%, without the benefit of knowing any patient's smoking history. Of the first 100 persons identified by the algorithm as being at risk and recruited for testing, 25 were proven to have previously undiagnosed COPD. CONCLUSIONS Pharmacy utilization increases in the years prior to initial COPD diagnosis. Algorithms based on pharmacy utilization can efficiently identify persons at risk for undiagnosed COPD.
Gaussian pixel weighting marks in amplitude modulation of color image watermarking

A watermark embedding method, using an amplitude modulation technique, based on Gaussian pixel-weighting marks is proposed. The method utilizes a technique of weighting a mark by averaging the luminance of its own pixel and its neighboring pixels, and uses it as an additional scaling factor in existing watermark embedding methods. The watermark retrieval process is borrowed from the technique of image averaging from the cross-shaped neighboring pixels of the watermarked image, and hence has no need of the original image. The results show that improved performance is obtained when applying the Gaussian pixel-weighting marks technique, compared to other techniques, namely the equal gain pixel-weighting and the no pixel-weighting marks techniques.
Observation on integron carriage among clinical isolates of Klebsiella pneumoniae producing extended-spectrum beta-lactamases.

PURPOSE Klebsiella pneumoniae is considered an important pathogen causing nosocomial and community-acquired infections and is often associated with the production of extended-spectrum beta-lactamases (ESBL) belonging to SHV and CTX-M families, which are frequently described as a part of complex integrons, facilitate their horizontal transfer to other related as well as unrelated microbes. The present study was undertaken to investigate the occurrence and characterization of integrons among K pneumoniae isolates producing ESBL in a tertiary referral hospital. MATERIALS AND METHODS A total of 136 clinical isolates of K pneumoniae were investigated for the presence of ESBL. Their ESBL genes were characterized by multiplex polymerase chain reaction (PCR). Integrase gene PCR was performed to detect the presence of integron. The isolates were further typed by random amplification of polymorphic DNA (RAPD). RESULT Out of 136 K pneumoniae isolates, 63 (46%) were confirmed to be ESBL producers. SHV (68%) and CTX-M (67%) ESBL genes were the most common in our study. Of the 63 ESBL-positive isolates, 58 (92%) strains carried integrons; 52 strains (82%) carried only class 1 integron, whereas 6 (9%) isolates harboured both class 2 integrons and the class 1 gene. However, in ESBL negatives, only 29 (40%) strains were positive for class 1 integron and none for class 2 integron. CONCLUSION The presence of class 2 integron amongst ESBL-producing K pneumoniae is being described for the first time in this part of the world. The findings of this study strongly suggest that integrons have a role in the dissemination of ESBL-mediated resistance among the nosocomial isolates of K pneumonia.
Temporomandibular Disorders: Moving from a Dentally Based to a Medically Based Model

INTRODUCTION The year 2000 marks the end of a century in which many I traditional dental concepts were subjected for the first time to some type of systematic inquiry. This kind of investigation produces results that differ considerably from the results of "Discovery" experiments (such as those often described in this section of JDR), in which new diseases or new diagnostic modalities are brought to light. This essay describes the background of nearly 40 years of systematic inquiry into the subject of temporomandibular disorders (TMD), much of which was directed at questioning the validity of the traditional concepts in this field, and how this eventually changed the clinical management of patients. It also recounts the struggle to persuade the dental profession to move from the past into the modem arena ofTMD diagnosis and treatment.
Input and output

A user interacts with an APL system through a session, an abstraction that represents a hypothetical machine capable of carrying out the evaluation sequences in this standard.The protocol for the use of a session takes the form of a dialogue: the user makes an entry and passes control to the APL system. The system processes the entry, produces a response, and returns control to the user.The user makes entries on a keyboard, and obtains responses by seeing them presented on a display-device. The combination of a keyboard and a display-device is intended to represent, abstractly, a terminal. This standard does not require the use of any particular terminal, keyboard, display or method of encoding characters. The ISO 2022.2 APL character encoding reproduced in Appendix A is widely used.The display-device is considered a window into a presentation-space, an unbounded sequence of past entries and responses. The mapping between the presentation-space and the display-device is not specified by this standard.The system obtains entries as tokens of class constant or interrupt by calling the session operation read-keyboard. It presents responses by calling the session operation display with a token of class result. The transformations from entry to token and from token to response are not specified by this standard, but certain desirable characteristics of these transformations are given as comments.Because the dialog protocol described here alternates between user and system, the session is always in one of two logical keyboard-states, open-keyboard or locked-keyboard, depending upon whether the user is making an entry or the system is producing a response. The user can request a change in keyboard-state from locked-keyboard to open-keyboard by using the signal-attention facility. In addition, the user can force a change in keyboard-state by signalling interrupt.
Why is there a Present-Day English absolute?

This paper examines the divergent evolutions of the Absolute Construction (AC) in the history of the Germanic languages, with a focus on English and Dutch, and provides an explanation of why only the English AC retained its frequency and productivity rate. Three language-internal factors are appealed to in order to account for this divergence: (i) increased with-augmentation of ACs results in fuzzy boundaries with the more frequently used gerunds as well as (regular) prepositional postmodifying constructions; (ii) the overall higher frequency in English of constructions with -ing-forms (gerunds, free adjuncts, and progressives) invites structural priming; and (iii) a possible typological shift of English from strictly bounded construal to a mixture of bounded and unbounded construal. An additional language-external factor is found in different prescriptivist traditions. English never really opposed the use of ACs whereas prescriptivism in other Germanic languages emphatically did.
The Pathogenesis of Autoimmune Liver Disease

Background: Autoimmune liver disease (AILD) encompasses 3 main distinct clinical diseases: autoimmune hepatitis, primary biliary cholangitis (formally known as cirrhosis, PBC) and primary sclerosing cholangitis (PSC). These conditions are an important, yet under-appreciated cause of patient morbidity and mortality with ongoing unmet needs for further research and clinical advances. Key Messages: There is observational evidence for genetic predisposition, with all 3 conditions being more common in first degree relatives. AILD is associated with the presence of auto-antibodies and higher risks of other non-hepatic auto-immune conditions. Genetic risk association studies have identified HLA and non-HLA risk loci for the development of disease, with some HLA loci providing prognostic information. This re-enforces the concept that genetic predisposition to autoimmunity is important, likely in the context of environmental exposures. Such environmental triggers are unclear but relevant risks include smoking, drug and xenobiotic exposure as well as the complexities of the microbiome. There is evidence for a loss of immune tolerance to self-antigens playing a part in the development of these conditions. In particular the IL-2 and IL-12 regulatory pathways have been implicated in pre-disposing to an unopposed inflammatory response within the liver. Main immunological themes revolve around loss of immune tolerance leading to T-cell mediated injury, imbalance in the regulation of immune cells and defective immune response to foreign antigens. For PBC and PSC, there is then the added complexity of the consequences of cholestasis on hepato-biliary injury, immune regulation and liver fibrosis. Conclusions: Whilst specific disease causes and triggers are still lacking, AILD arises on the background of collective genetic and environmental risk, leading to chronic and abnormal hepato-biliary immune responses. Effective and more rational therapy will ultimately be developed when the multiple pathways to liver injury are better understood.