gebhart/patrepeval huggingface dataset:
Development and Application of a Real-Time PCR Approach for Quantification of Uncultured Bacteria in the Central Baltic Sea (2004)

We have developed a highly sensitive approach to assess the abundance of uncultured bacteria in water samples from the central Baltic Sea by using a noncultured member of the "Epsilonproteobacteria" related to Thiomicrospira denitrificans as an example. Environmental seawater samples and samples enriched for the target taxon provided a unique opportunity to test the approach over a broad range of abundances. The approach is based on a combination of taxon- and domain-specific real-time PCR measurements determining the relative T. denitrificans-like 16S rRNA gene and 16S rRNA abundances, as well as the determination of total cell counts and environmental RNA content. It allowed quantification of T. denitrificans-like 16S rRNA molecules or 16S rRNA genes as well as calculation of the number of ribosomes per T. denitrificans-like cell. Every real-time measurement and its specific primer system were calibrated using environmental nucleic acids obtained from the original habitat for external standardization. These standards, as well as the respective samples to be measured, were prepared from the same DNA or RNA extract. Enrichment samples could be analyzed directly, whereas environmental templates had to be preamplified with general bacterial primers before quantification. Preamplification increased the sensitivity of the assay by more than 4 orders of magnitude. Quantification of enrichments with or without a preamplification step yielded comparable results. T. denitrificans-like 16S rRNA molecules ranged from 7.1 x 10(3) to 4.4 x 10(9) copies ml(-1) or 0.002 to 49.7% relative abundance. T. denitrificans-like 16S rRNA genes ranged from 9.0 x 10(1) to 2.2 x10(6) copies ml(-1) or 0.01 to 49.7% relative abundance. Detection limits of this real-time-PCR approach were 20 16S rRNA molecules or 0.2 16S rRNA gene ml(-1). The number of ribosomes per T. denitrificans-like cell was estimated to range from 20 to 200 in seawater and reached up to 2,000 in the enrichments. The results indicate that our real-time PCR approach can be used to determine cellular and relative abundances of uncultured marine bacterial taxa and to provide information about their levels of activity in their natural environment.
A Linear Time Varying Model for On-Off Valve Controlled Pneumatic Actuators (1990)

A new linear time varing (LTV) model has been developed for open loop, on-off valve controlled pneumatic actuation systems. This formulation is based on a periodic profile description for variable operating points and directional control valve flow variations. The dynamic behavior of the example case, a single acting cylinder controlled by a two way-two port rotary valve, under the cyclic pressure loading is obtained using the proposed LTV model. Experimental evidence and digital simulation predictions based on the nonlinear mathematical equations validate the analytical formulation. The proposed LTV model is found to be better and more applicable than linear time invariant (LTI) models used previously by many investigators.
Hepatitis B virus DNA levels and outcomes in chronic hepatitis B # † (2009)

Serum hepatitis B virus (HBV) DNA levels can fluctuate markedly during the course of chronic HBV infection. Both case-control and cohort studies have shown a significant, dose-response association between serum HBV DNA levels measured at the time of initial evaluation and the subsequent risk of cirrhosis. A similar direct relationship has been shown for the risk of hepatocellular carcinoma (HCC) in cross-sectional, case-control, and cohort studies. Interventional studies have shown a strong correlation between the indices of disease activity seen on liver biopsy and levels of serum HBV DNA. These studies have also shown that reduction in HBV DNA levels correlate strongly with improvements in liver histology. For patients with HCC, prognosis (including risk of death, metastasis, and recurrence following surgery) is worse with higher serum HBV DNA levels. The preponderance of the evidence in the published literature demonstrates that serum HBV DNA level is an important and independent risk factor for disease progression in chronic hepatitis B. The relative importance of serial HBV DNA measurements, the loss of hepatitis B e and surface antigens, as well as the emergence of HBV mutants in the progression of chronic hepatitis B, especially in young patients, is an important need for future research.
Analysis of Protein Complexes in Wheat Amyloplasts Reveals Functional Interactions among Starch Biosynthetic Enzymes    (2008)

Protein-protein interactions among enzymes of amylopectin biosynthesis were investigated in developing wheat (Triticum aestivum) endosperm. Physical interactions between starch branching enzymes (SBEs) and starch synthases (SSs) were identified from endosperm amyloplasts during the active phase of starch deposition in the developing grain using immunoprecipitation and cross-linking strategies. Coimmunoprecipitation experiments using peptide-specific antibodies indicate that at least two distinct complexes exist containing SSI, SSIIa, and either of SBEIIa or SBEIIb. Chemical cross linking was used to identify protein complexes containing SBEs and SSs from amyloplast extracts. Separation of extracts by gel filtration chromatography demonstrated the presence of SBE and SS forms in protein complexes of around 260 kD and that SBEII forms may also exist as homodimers. Analysis of cross-linked 260-kD aggregation products from amyloplast lysates by mass spectrometry confirmed SSI, SSIIa, and SBEII forms as components of one or more protein complexes in amyloplasts. In vitro phosphorylation experiments with gamma-(32)P-ATP indicated that SSII and both forms of SBEII are phosphorylated. Treatment of the partially purified 260-kD SS-SBE complexes with alkaline phosphatase caused dissociation of the assembly into the respective monomeric proteins, indicating that formation of SS-SBE complexes is phosphorylation dependent. The 260-kD SS-SBEII protein complexes are formed around 10 to 15 d after pollination and were shown to be catalytically active with respect to both SS and SBE activities. Prior to this developmental stage, SSI, SSII, and SBEII forms were detectable only in monomeric form. High molecular weight forms of SBEII demonstrated a higher affinity for in vitro glucan substrates than monomers. These results provide direct evidence for the existence of protein complexes involved in amylopectin biosynthesis.
Fabrication of “18 Weave” Muscles and Their Application to Soft Power Support Suit for Upper Limbs Using Thin McKibben Muscle (2019)

In this letter, we propose a novel active weave named “18 Weave” using a thin McKibben muscle and report on the application to a prototype soft power support suit for the upper limb. The active weave utilizes the flexibility of the thin McKibben muscle, which is used for warps and wefts. From the proposed structure, we confirmed that a 19.4% additional displacement is achieved compared to a single artificial muscle. The flexible and lightweight assistance suit can be realized with the active weave that has advantages of flexibility and shape adaptability. We confirmed the compliance and fatigue alleviation effect of the suit. Measurements of the myopotentials confirmed significant decreases in the activities of the anterior deltoid, posterior deltoid, biceps brachii, and triceps brachii muscles in their integrated electromyogram (iEMG).
Alfabetización Académica: Un Cambio Necesario, algunas Alternativas Posibles (2003)

Academy reading? So basic a process in higher education? A remedial need to palliate that which has not been done in the previous school levels? Once again, some body that propose a reading and writing workshop to the freshmen? To tranquilize the audience, I will make myself clear, in the first place that I do not assume, in this exposition, the assumptions of these anticipated questions, but debate them. For this, I review the literature on academic literacy, pointing out the explicative power to account for the reading and writing, wasted in our universities, that do not offer the context in which student would write for learning. I synthesize the results of observations in 90 Australian, Canadian and American universities in which, contrarily to our institutions, have implemented a variety of systems to literate students academically. Finally, I conclude showing the institutional and curricular changes that higher education institutions require to assume the task of transmitting the writing culture intrinsic to the professions they teach.
Decision support and training system for management of endodontically treated teeth (2014)

Endodontically treated teeth are often structurally compromised and require proper prosthodontic restoration following endodontic therapy to ensure long-term success. As a result and as the number of endodontic procedures in contemporary dentistry have steadily increased in the past decade, tooth restoration is becoming an integral part of restorative practice in everyday dentistry. Although the subject has been widely researched and published in dental literature, the topic of best way to restore root canal treated teeth still remains an area prone to high error rates in decision-making. Complexity of the domain is largely due to multi-factorial considerations and need for evaluation of a wide range of restorative techniques of varying intricacies. Determining the best restorative treatment plan following endodontic therapy requires sound knowledge of principles that span across multiple dental disciplines of endodontics, orthodontics, periodontics, and prosthodontics. Memorization of a large and ever-increasing number of decision rules to be meaningfully used at the point-of-care can be arduous, especially for dental students and less experienced clinicians. Clinical experts with their knowledge and years of experience treating patients can help in the process, but may not always be around to provide assistance. Misdiagnosis and mistreatment of such teeth can lead to adverse clinical consequences and significant inconvenience to the patient as well as financial implications both for the patient and provider. To address this problem, we have developed a clinical decision support and training system based on expert knowledge and evidence-based guidelines. Using Corvid expert system development framework and careful consideration of factors necessary for success of clinical decision support systems, we have developed a working prototype of a web-based, interactive system that can be launched at the operatory and can be easily integrated into providers’ workflow. One of the important goals of the system is to train users to think holistically like an expert while problem-solving and planning restorative treatment. Based on information entered by the user, system comes up with recommendations, alerts and treatment prognosis. Treatment options provided with justifying explanations can help clinicians provide decision-making rationale to the patients, better inform and educate them, and thus better manage their expectations and ensure their satisfaction and compliance. Since the knowledge base of our system is developed using expert guidelines that are known to be effective, we expect to see improved restorative treatment outcomes for endodontically treated teeth.
The enigma of rosacea (2007)

This short paper reviews the nature of rosacea emphasizing the possibility of a solar cause. The sites of involvement and the physical signs of rosacea including the flushing, the erythema and the telangiectasia as well as the intermittent episodes of inflammation with swelling and papules may all be explained by UVR induced damage to dermal connective tissue. The dermal damage permits vaso-dilation and vascular pooling.
Effects of Long‐Acting Versus Short‐Acting Calcium Channel Blockers Among Older Survivors of Acute Myocardial Infarction (1999)

Use of long-acting dihydropyridine calcium channel blockers after acute MI was associated with substantially lower rates of cardiac rehospitalization and death compared with use of their short-acting counterparts. More data are needed to address the possibility that long-acting, compared with short-acting, non-dihydropyridines could decrease rehospitalization rates but increase mortality.
A 3.9-/spl mu/m pixel pitch VGA format 10-b digital output CMOS image sensor with 1.5 transistor/pixel (2004)

A 3.9-/spl mu/m pixel pitch VGA format 10-b digital output CMOS image sensor with 1.5 transistor/pixel has been developed for mobile applications. The newly developed CMOS pixel architecture realizes the minimum number of the transistors in one pixel. Small pixel size and sufficient fill factor are achieved by using the shared pixel architecture and floating diffusion driving. High conversion gain, low random noise, and low dark current are achieved by buried photodiode with complete charge transfer capability and correlated double sampling (CDS) circuit. The image sensor is fabricated in a thin planarized 0.35-/spl mu/m single poly-Si double-metal customized CMOS process in order to provide good image performance. The image sensor achieves low noise floor of 330 /spl mu/V and low dark current of 50 pA/cm/sup 2/ at 45/spl deg/C. This image sensor also realized various functions by on-chip digital and analog circuits.
Using AUC and accuracy in evaluating learning algorithms (2005)

The area under the ROC (receiver operating characteristics) curve, or simply AUC, has been traditionally used in medical diagnosis since the 1970s. It has recently been proposed as an alternative single-number measure for evaluating the predictive ability of learning algorithms. However, no formal arguments were given as to why AUC should be preferred over accuracy. We establish formal criteria for comparing two different measures for learning algorithms and we show theoretically and empirically that AUC is a better measure (defined precisely) than accuracy. We then reevaluate well-established claims in machine learning based on accuracy using AUC and obtain interesting and surprising new results. For example, it has been well-established and accepted that Naive Bayes and decision trees are very similar in predictive accuracy. We show, however, that Naive Bayes is significantly better than decision trees in AUC. The conclusions drawn in this paper may make a significant impact on machine learning and data mining applications.
New concepts in the pathogenesis, diagnosis and control of diseases caused by the bovine viral diarrhea virus. (1988)

The new information on the pathogenesis and epidemiology of mucosal disease of cattle is reviewed. It is now known that clinical mucosal disease occurs only in cattle which were infected with a pestivirus in early gestation and were born with persistent viral infection and specific immunotolerance. These animals may be clinically normal at birth but may develop fatal mucosal disease, perhaps following superinfection with another pestivirus, usually between 6 and 24 months of age. They may also remain clinically normal indefinitely and breed successfully. The progeny from persistently infected females will similarly be persistently viremic, and maternal families of such animals may be established.Congenital defects may occur when infection of the fetus occurs in mid-gestation. Although fetuses may be infected in utero in late gestation, the infections do not persist, the fetuses develop antibodies, and they appear to suffer no ill-effects. Postnatal infection can result in subclinical disease (bovine viral diarrhea) with a normal immune response; the virus may also be responsible for enhanced susceptibility to other infections, diarrhea in newborn calves, and reproductive failure.Prevention of the economically important diseases caused by the virus is dependent upon the identification and elimination of persistently viremic animals, which are reservoirs of infection, and the vaccination of immunocompetent females at least three weeks before breeding. However, because of serotypic differences between strains, there is some doubt whether vaccination will reliably provide protection against the transplacental fetal infections that are important in the pathogenesis of this disease. There is no substantial evidence to warrant the vaccination of feedlot cattle.
Optimizing for parallelism and data locality (2014)

Previous research has used program transformation to introduce parallelism and to exploit data locality. Unfortunately, these two objectives have usually been considered independently. This work explores the trade-offs between effectively utilizing parallelism and memory hierarchy on shared-memory multiprocessors. We present a simple, but surprisingly accurate, memory model to determine cache line reuse from both multiple accesses to the same memory location and from consecutive memory access. The model is used in memory optimizing and loop parallelization algorithms that effectively exploit data locality and parallelism in concert. We demonstrate the efficacy of this approach with very encouraging experimental results.
Limb, genital, CNS, and facial malformations result from gene/environment-induced cholesterol deficiency: Further evidence for a link to sonic hedgehog (1997)

Low cholesterol levels produced by treating cholesterol deficient mutant mice with a cholesterol synthesis inhibitor (BM 15.766) between days 4 to 7 of pregnancy resulted in malformations consistent with those in the Smith-Lemli-Opitz syndrome (SLOS). Facial anomalies in mildly affected gestational day 12 mouse embryos included a small nose and long upper lip; in more severely affected embryos, the facial and forebrain anomalies are representative of holoprosencephaly. Additionally, abnormalities of the mid- and hind-brain were observed and included stenosis of the cerebral aqueduct at the level of the isthmus and apparent absence of the organ progenitor for the cerebellar vermis. Although not previously directly linked to cholesterol deficiency in experimental animals, limb and external genital defects were a notable outcome in this multifactorially-based cholesterol deficiency model. The results of this study provide new evidence supporting an important role for cholesterol in early embryonic development, provide additional support for the hypothesis that this role may involve the function of specific gene products, such as sonic hedgehog (shh) signaling protein, and provide a description of the pathogenesis of some of the characteristic malformations in SLOS.
An extended multi-zone combustion model for PCI simulation (2011)

Novel combustion modes are becoming an important area of research with emission regulations more stringent than ever before, and with fuel economy being assigned greater importance every day. Homogeneous Charge Compression Ignition (HCCI) and Premixed Compression Ignition (PCI) modes in particular promise better fuel economy and lower emissions in internal combustion engines. Multi-zone combustion models have been popular in modelling HCCI combustion. In this work, an improved multi-zone model is suggested for PCI combustion modelling. A new zoning scheme is suggested based on incorporating the internal energy of formation into an earlier conventional HCCI multi-zone approach, which considers a two-dimensional reaction space defined by equivalence ratio and temperature. It is shown that the added dimension improves zoning by creating more representative zones, and thus reducing errors compared to the conventional zoning approach, when applied to PCI simulation.
Clinical Features and Natural History of Nonalcoholic Steatosis Syndromes (2001)

Nonalcoholic steatohepatitis, along with other forms of nonalcoholic fatty liver disease, is a chronic liver disease that is attracting increasing significance. It is a clinicopathologic syndrome that was originally described in obese, diabetic females who denied alcohol use but in whom the hepatic histology was consistent with alcoholic hepatitis. This typical patient profile has been expanded and is now recognized to occur even in normal weight males without overt abnormalities in carbohydrate metabolism. Although originally believed to be a benign clinical entity, nonalcoholic steatohepatitis is now recognized as a cause of progressive fibrotic liver disease with adverse clinical sequelae. It is important to emphasize that nonalcoholic steatohepatitis is best considered one type of a larger spectrum of nonalcoholic fatty liver disease that is a consequence of insulin resistance and ranges from fat alone to fat plus inflammation, fat plus ballooning degeneration, and nonalcoholic steatohepatitis, the latter being the most serious form. As with any disease, the clinical importance of nonalcoholic steatohepatitis is related to its prevalence and natural history. Recent studies using different methodologies indicate that in the general population the prevalence of fatty liver and nonalcoholic steatohepatitis is approximately 20% and 3%, respectively. These prevalence rates are increased in certain subpopulations such as obesity and type II diabetes. Of greater concern is the recognition that cirrhosis and liver-related deaths occur in approximately 20% and 8% of these patients, respectively, over a 10-year period. Risk factors for these adverse clinical symptoms include patients older than the age of 45, the presence of diabetes or obesity, an aspartate aminotransferase/alanine aminotransferase ratio > 1 and hepatic histology. However, a number of important unresolved issues must be clarified before the true natural history of this disease can be fully understood.
Design of a portable wide field of view GPU-accelerated multiphoton imaging system for real-time imaging of breast surgical specimens (2016)

We present a portable multiphoton system designed for evaluating centimeter-scale surgical margins on surgical breast specimens in a clinical setting. The system is designed to produce large field of view images at a high frame rate, while using GPU processing to render low latency, video-rate virtual H&E images for real-time assessment. The imaging system and virtual H&E rendering algorithm are demonstrated by imaging unfixed human breast tissue in a clinical setting.
Algorithms for Maximum Power Point Tracking through Load Management (2021)

This paper presents the basic control algorithm and its improvements for a feedback-based load-matching PV system. Our previous load-matching system employed a photodetector for system control. Several practical challenges for the photodetector-based load-matching system have been identified. The feedback-based system eliminates those challenges and makes the system practical. The methods for improving the basic algorithm include monitoring PV power over time, a time delay between two power measurements, averaging multiple power measurements, and a power threshold before attempting a switch. They are implemented in SIMULINK for a system with six equal-resistance loads on both sunny and cloudy days and the optimal values for these parameters are identified. The algorithm with optimized parameters is verified in a real system on both sunny and cloudy days. These results prove the viability of maximum power point tracking through load management.