gebhart/patrepeval huggingface dataset:
T cell priming in vivo: a major role for B cells in presenting antigen to T cells in lymph nodes. (1987)

Previous studies have shown that lymph node (LN) T cells from mice given repeated injections of anti-mu antisera from birth (mu sm) fail to mount secondary T proliferative responses to antigen in vitro after s.c. priming in vivo. This finding raised the possibility that priming of T cells in LN depends on the presence of B cells, Ig+ B lymphocytes being absent in mu sm. In support of this idea, the present paper shows that the priming defect in LN of mu sm can be largely overcome by injecting B cell populations s.c. 1 day before s.c. priming with antigen. Restoration of LN priming was observed with s.c. injection of highly purified populations of small B cells but not with heat-killed or lightly irradiated B cells. Homing studies indicated that approximately 10% of s.c.-injected B cells reached the draining LN. In other studies, irradiated mice injected i.v. with purified T cells manifested poor priming in LN after s.c. injection of antigen. It was reasoned that the LN priming defect in this situation reflected the lack of B cells in irradiated mice, B cells being highly radiosensitive. In support of this notion, it was found that s.c. injection of B cells into irradiated recipients of T cells led to high priming of T cells in LN after s.c. injection of antigen. Although T cells exposed to antigen in B-depleted LN of mu sm and irradiated mice gave negligible T proliferative responses in vitro, low but significant levels of primed T helper function were detected in a sensitive T helper assay in vivo. In light of this finding, our working hypothesis is that the initial induction of T cells to antigen in LN is controlled by resident dendritic cells (or other non-B antigen-presenting cells), the main role of B cells being to control the clonal expansion of activated T cells.
Indirect pharmacodynamic response models do not require any parametric pharmacokinetic model to be fitted to effect-time data. (1997)

Indirect response models (IRM) represent one of the possible ways to explain and quantitatively describe a delayed pharmacodynamic effect at non-steady-state conditions. The standard way to get estimates of pharmacodynamic (PD) parameters of IRM consists of two steps. First, an appropriate parametric pharmacokinetic (PK) model (compartmental, polyexponential, etc.) is to be fitted to plasma concentration-time data, and then IRM is fitted to PD data having PD model as an input. In the present work it is demonstrated that a simple piecewise function which consists in interpolation lines connecting concentration-time points can be used as a universal nonparametric PK model thereby allowing to skip the first step. MS Excel spreadsheets implementing this PK model and four known versions of IRM are presented. The usefulness of the approach is demonstrated by fitting IRMs to simulated data as well as to real PK/PD data of warfarin and terbutaline. Estimates of IRM parameters obtained with the nonparametric PK model were close to that published in the literature.
Near infrared imaging of teeth at wavelengths between 1200 and 1600 nm (2011)

Near-IR (NIR) imaging is a new technology that is currently being investigated for the detection and assessment of dental caries without the use of ionizing radiation. Several papers have been published on the use of transillumination and reflectance NIR imaging to detect early caries in enamel. The purpose of this study was to investigate alternative near infrared wavelengths besides 1300-nm in the range from 1200-1600-nm to determine the wavelengths that yield the highest contrast in both transmission and reflectance imaging modes. Artificial lesions were created on thirty tooth sections of varying thickness for transillumination imaging. NIR images at wavelengths from the visible to 1600-nm were also acquired for fifty-four whole teeth with occlusal lesions using a tungsten halogen lamp with several spectral filters and a Ge-enhanced CMOS image sensor. Cavity preparations were also cut into whole teeth and Z250 composite was used as a restorative material to determine the contrast between composite and enamel at NIR wavelengths. Slightly longer NIR wavelengths are likely to have better performance for the transillumination of occlusal caries lesions while 1300-nm appears best for the transillumination of proximal surfaces. Significantly higher performance was attained at wavelengths that have higher water absorption, namely 1460-nm and wavelengths greater than 1500-nm and these wavelength regions are likely to be more effective for reflectance imaging. Wavelengths with higher water absorption also provided higher contrast of composite restorations.
Expression of the enhancer of zeste homolog 2 is correlated with poor prognosis in human gastric cancer (2006)

Overexpression of the enhancer of zeste homolog 2 (EZH2) protein, a known repressor of gene transcription, has been reported to be associated with biological malignancy of prostate cancer and several other cancers. The purpose of this study was to examine the expression of EZH2 and analyze its relationship with the clinicopathological features of human gastric cancers. Expression levels of EZH2 mRNA and protein were examined in 13 gastric cancer cell lines and in 83 surgically removed human gastric cancer tissues. Immunohistochemical analysis of the 83 tissue samples and corresponding non‐cancerous gastric mucosa showed that EZH2 was more highly expressed in the cancerous than in the non‐cancerous tissues, and the expression levels of EZH2 were highly correlated with tumor size, depth of invasion, vessel invasion, lymph node metastasis and clinical stages. Univariate analysis of survival rate calculated by the Kaplan‐Meier method revealed that gastric cancer patients with high‐level EZH2 expression had poorer prognosis than those expressing no or low levels of EZH2 ( P = 0.0271). These findings suggest that overexpression of EZH2 may contribute to the progression and oncogenesis of human gastric cancers, and thus immunohistochemical study of EZH2 expression may serve as a new biomarker for predicting the prognosis of gastric cancers. ( Cancer Sci 2006; 97: 484 – 491)
A digital licensing model for the exchange of learning objects in a federated environment (2004)

In this paper, we present a model for a licensing scheme that allows the expression, negotiation and management of digital rights, in a federated object-sharing environment. We first discuss motivations and issues around digital rights management (DRM), we then describe the DRM implementation for the celebrate project, and propose an extension to the celebrate model in order to take into account licenses as opposed to individual rights.
Phase II Study of Vinorelbine Plus Trastuzumab in HER2 Overexpressing Metastatic Breast Cancer Pretreated with Anthracyclines and Taxanes (2011)

These results show that a combination chemotherapy consisting of vinorelbine and trastuzumab is useful in patients with HER2-overexpressing metastatic breast cancer who were pretreated with anthracyclines and taxanes, with a favorable toxicity profile.
The Role of Human HtrA1 in Arthritic Disease (2005)

Human HtrA1 belongs to a widely conserved family of serine proteases involved in various aspects of protein quality control and cell fate. Although HtrA1 has been implicated in the pathology of several diseases, its precise biological functions remain to be established. Through identification of potential HtrA1 targets, studies presented herein propose that within the context of arthritis pathology HtrA1 contributes to cartilage degradation. Elevated synovial HtrA1 levels were detected in fluids obtained from rheumatoid and osteoarthritis patients, with synovial fibroblasts identified as a major source of secreted HtrA1. Mass spectrometry analysis of potential HtrA1 substrates within synovial fluids identified fibronectin as a candidate target, and treatment of fibronectin with recombinant HtrA1 led to the generation of fibronectin-degradation products that may be involved in cartilage catabolism. Consistently, treatment of synovial fibroblasts with HtrA1 or HtrA1-generated fibronectin fragments resulted in the specific induction of matrix metalloprotease 1 and matrix metalloprotease 3 expression, suggesting that HtrA1 contributes to the destruction of extracellular matrix through both direct and indirect mechanisms.
Sequence of thioredoxin reductase from Escherichia coli. Relationship to other flavoprotein disulfide oxidoreductases. (1988)

The DNA sequence of the Escherichia coli gene encoding thioredoxin reductase has been determined. The predicted protein sequence agrees with an earlier determination of the 17 amino-terminal amino acids and with a fragment of the protein containing the redox-active half-cystines. Similarity between E. coli thioredoxin reductase and other flavoprotein disulfide oxidoreductases is quite limited, but three short segments, two of which are probably involved in FAD and NADPH binding, are highly conserved between thioredoxin reductase, glutathione reductase, dihydrolipoamide dehydrogenase, and mercuric reductase.
Deep wet etching on fused silica material for fiber optic sensors (2004)

In this paper, deep microstructures on fused silica material, which are useful for fabrication of the fiber optic sensors, were obtained by using a wet chemical etching process. The etching solutions and the masking materials used for developing deep structure are described in this paper. The etch rate of a fused silica diaphragm in room temperature ranged from 46nm per minute to 83nm per minute with different concentrations of Buffered Hydrogen Fluoride (BHF). The etch depth of one step etching was 25&mu;m with the surface roughness less than 20nm (peak-to-peak value). The optical reflectance from the deep etched surface was 4%, which is the same as a well-cleaved fiber end face. This result made the visibility of interference fringes from the single mode fiber optic sensors to be as high as 96%. Furthermore, two-step structures on the fused silica diaphragms with the total depth greater than 35&mu;m are demonstrated. To the best knowledge of the authors, this is the deepest structure produced by wet etching process on fused silica material. Fiber optic pressure sensors based on deep etched diaphragms were fabricated and tested. Fabrication of microstructures on the fiber end faces by using this process is therefore possible.
[Antibiotic resistance here to stay? Compensatory mutations restore virulence of resistant bacteria]. (1998)

Bacterial antibiotic resistance has increased alarmingly because of overuse of antibiotics both in humans and animals. One way of reversing this development is to reduce the use of antibiotics, thus promoting the disappearance of the resistant bacteria already present in humans and the environment. This approach is based on the assumption that resistance is conferred at the cost of impaired survival fitness in the absence of antibiotics, as compared with sensitive strains. It seems to be generally true that resistant bacteria are less fit than the respective sensitive strains, which suggests that resistance may be reversible. However, a complicating factor is the frequent finding in resistant strains of various types of compensatory mutations that restore fitness without concomitant loss of resistance. Thus, second-site compensatory mutations may allow resistant strains to persist and compete successfully with sensitive strains even in an environment depleted of antibiotics. It is concluded in the article that, if compensatory mutations are as common in clinical settings as they are in the laboratory, many types of resistance will be irreversible.
Automatic detection of pain intensity (2012)

Previous efforts suggest that occurrence of pain can be detected from the face. Can intensity of pain be detected as well? The Prkachin and Solomon Pain Intensity (PSPI) metric was used to classify four levels of pain intensity (none, trace, weak, and strong) in 25 participants with previous shoulder injury (McMaster-UNBC Pain Archive). Participants were recorded while they completed a series of movements of their affected and unaffected shoulders. From the video recordings, canonical normalized appearance of the face (CAPP) was extracted using active appearance modeling. To control for variation in face size, all CAPP were rescaled to 96×96 pixels. CAPP then was passed through a set of Log-Normal filters consisting of 7 frequencies and 15 orientations to extract 9216 features. To detect pain level, 4 support vector machines (SVMs) were separately trained for the automatic measurement of pain intensity on a frame-by-frame level using both 5-folds cross-validation and leave-one-subject-out cross-validation. F1 for each level of pain intensity ranged from 91% to 96% and from 40% to 67% for 5-folds and leave-one-subject-out cross-validation, respectively. Intra-class correlation, which assesses the consistency of continuous pain intensity between manual and automatic PSPI was 0.85 and 0.55 for 5-folds and leave-one-subject-out cross-validation, respectively, which suggests moderate to high consistency. These findings show that pain intensity can be reliably measured from facial expression in participants with orthopedic injury.
[Observation on revascularization of free flaps with the technique of microvascular corrosion] (1997)

In order to study the process of revascularization of free flap bilateral dorsal-auricular free flaps of 18 Newzealand rabbits were completed and investigated with the technique of microvascular corrosion casting at 2,4,7,10 days and 2,4 weeks postoperatively.It was discovered that scarce neovascularity appeared around the margin of flap before 2 weeks following transplantation and extensive revascularization occured at 3 weeks postoperatively.The capillaries connected through their netword expansion while central artery and vein formed recirculation by means of multiple point anastomoses of the "vascular buds" sprouting up at both ends of vessels.
BRAF mutations in metastatic melanoma: a possible association with clinical outcome. (2003)

Our results, besides confirming the high frequency of BRAF mutations in metastatic melanomas, also underline the potential importance of these mutations in disease outcome.
COMPARISON OF TWO INJECTION TECHNIQUES USING BOTULINUM TOXIN IN SPASTIC HEMIPLEGIA1 (1996)

This study sought to test the hypothesis that injections of botulinum toxin type A (BTX-A) at the mid belly of the gastrocnemius muscle in spastic hemiplegic adults produce superior clinical results to proximal injections directed toward the muscular origin. We designed a randomized, double-blind, placebo-controlled intervention study at a university tertiary care setting. Seventeen subjects with chronic spastic hemiplegic gait were enrolled from a volunteer community sample; time range from acute neurologic insult was 0.75 to 31 yr; age range was 19 to 71 yr; gender consisted of 11 men and 4 women; diagnoses were 12 patients with stroke, 2 with traumatic brain injuries, and 1 with a brain tumor. Two subjects were withdrawn from the study because of (1) acute vascular occlusion before intervention and (2) noncompliance with follow-up visits. After baseline measurements, subjects were injected with 50 units of BTX-A (volume, 0.5 cc) into the medial or lateral gastrocnemius: (1) proximally at one site near the muscular origin; (2) distally at three sites along the mid belly. We measured outcome using the Fugl-Meyer score, Ashworth scale, ankle range of motion, and a timed 50-ft fastest walk. No outcome measures showed a significant effect attributable to site of injections. Confounding variables included physical therapy and varying duration of illness in the study cohort. We conclude that the results failed to support the hypothesis that BTX-A injections at the mid belly of the gastrocnemius produced superior functional improvements to injections located near the muscular origin using localization techniques described. Additional research comparing more precise localization methods for BTX-A injections might further establish the importance of electromyographic guidance using BTX-A in management of spasticity.
Getting Acquainted with Fractals (2007)

This well-written book provides a mathematically oriented introduction to fractals, with a focus upon three types of fractals: fractals of curves, attractors for iterative function systems in the plane, and Julia sets. The presentation is on an undergraduate level, with an ample presentation of the corresponding mathematical background, e.g., linear algebra, calculus, algebra, geometry, topology, measure theory and complex analysis. The book contains over 100 colour illustrations. A mathematically oriented introduction to fractals. Focus upon three types of fractals: Fractals of curves, attractors for iterative function systems in the plane, and Julia sets. The presentation is on an undergraduate level, with an ample presentation of the corresponding mathematical background. Contains over 100 coloured illustrations.
Free breathing 3D balanced FFE coronary magnetic resonance angiography with prolonged cardiac acquisition windows and intra‐RR motion correction (2005)

A shortcoming of today's coronary magnetic resonance angiography (MRA) is its low total scan efficiency (<5%), as only small well-defined fractions of the respiratory (50%) and cardiac (10%) cycle are used for data acquisition. These precautions are necessary to prevent blurring and artifacts related to respiratory and cardiac motion. Hence, scan times range from 4 to 9 min, which may not be tolerated by patients. To overcome this drawback, an ECG-triggered, navigator-gated free breathing radial 3D balanced FFE sequence with intra-RR motion correction is investigated in this study. Scan efficiency is increased by using a long cardiac acquisition window during the RR interval. This allows the acquisition of a number of independent k-space segments during each cardiac cycle. The intersegment motion is corrected using a self-guided epicardial fat tracking procedure in a postprocessing step. Finally, combining the motion-corrected segments forms a high-resolution image. Experiments on healthy volunteers are presented to show the basic feasibility of this approach.
The role of the complement system in shock and tissue injury induced by tumour necrosis factor and endotoxin. (1990)

It has previously been shown that tumour necrosis factor-alpha (TNF), together with bacterial lipopolysaccharide (LPS), induces shock and bowel necrosis in the rat. Since the complement system plays an important role in inflammation and tissue injury, its role has been studied in a similar model in mice. In most of the present experiments, a low dose (0.2 micrograms/g) of TNF was used for priming, followed 30 min later by LPS (3 micrograms/g), and the experiment was terminated in 150 min. It is shown that: (i) TNF exerts no systemic effects by itself; LPS elicits only mild hypotension but causes no lethality; (ii) TNF-primed mice show exaggerated effects of shock, hypothermia, haemoconcentration and bowel injury after LPS; the majority of these mice died within 150 min; (iii) administration of LPS alone mildly activates the complement system in vivo, while TNF alone has no effect; (iv) the effects of TNF and LPS on complement activation are synergistic; (v) the acute development of shock and bowel injury in response to TNF-LPS is dependent on an intact complement system, more specifically C5, since C5-deficient mice were protected from TNF-LPS-induced shock and tissue injury; C5-deficient mice also showed less hypotension, hypothermia, haemoconcentration and better intestinal perfusion compared with C5-sufficient animals; (vi) however, when the priming dose of TNF was raised to 0.5 micrograms/g, most of the C5-deficient mice developed marked hypothermia, hypotension, haemoconcentration, bowel injury and died. Thus, it is concluded that TNF and LPS act synergistically in activating the complement system, which plays an important role in mediating the tissue injury and lethality induced by these agents.
Biology of Bacilli. Applications to industry. (1992)

What is a bacillus? germination transcriptional regulation of gene expression heterologous gene expression control of post-exponential gene expression by transition state regulators molecular cloning protein export and development of secretion vectors extracellular enzymes bacterial insect toxins development of genetic engineering in bacillus megaterium - an example of the versatility and potential of industrially important bacilli production of commercially valuable products (a summary).
Homeobox gene expression profile indicates HOXA5 as a candidate prognostic marker in oral squamous cell carcinoma (2011)

The search for molecular markers to improve diagnosis, individualize treatment and predict behavior of tumors has been the focus of several studies. This study aimed to analyze homeobox gene expression profile in oral squamous cell carcinoma (OSCC) as well as to investigate whether some of these genes are relevant molecular markers of prognosis and/or tumor aggressiveness. Homeobox gene expression levels were assessed by microarrays and qRT-PCR in OSCC tissues and adjacent non-cancerous matched tissues (margin), as well as in OSCC cell lines. Analysis of microarray data revealed the expression of 147 homeobox genes, including one set of six at least 2-fold up-regulated, and another set of 34 at least 2-fold down-regulated homeobox genes in OSCC. After qRT-PCR assays, the three most up-regulated homeobox genes (HOXA5, HOXD10 and HOXD11) revealed higher and statistically significant expression levels in OSCC samples when compared to margins. Patients presenting lower expression of HOXA5 had poorer prognosis compared to those with higher expression (P=0.03). Additionally, the status of HOXA5, HOXD10 and HOXD11 expression levels in OSCC cell lines also showed a significant up-regulation when compared to normal oral keratinocytes. Results confirm the presence of three significantly upregulated (>4-fold) homeobox genes (HOXA5, HOXD10 and HOXD11) in OSCC that may play a significant role in the pathogenesis of these tumors. Moreover, since lower levels of HOXA5 predict poor prognosis, this gene may be a novel candidate for development of therapeutic strategies in OSCC.
Recognizing Facial Expression: Machine Learning and Application to Spontaneous Behavior (2005)

We present a systematic comparison of machine learning methods applied to the problem of fully automatic recognition of facial expressions. We report results on a series of experiments comparing recognition engines, including AdaBoost, support vector machines, linear discriminant analysis. We also explored feature selection techniques, including the use of AdaBoost for feature selection prior to classification by SVM or LDA. Best results were obtained by selecting a subset of Gabor filters using AdaBoost followed by classification with support vector machines. The system operates in real-time, and obtained 93% correct generalization to novel subjects for a 7-way forced choice on the Cohn-Kanade expression dataset. The outputs of the classifiers change smoothly as a function of time and thus can be used to measure facial expression dynamics. We applied the system to to fully automated recognition of facial actions (FACS). The present system classifies 17 action units, whether they occur singly or in combination with other actions, with a mean accuracy of 94.8%. We present preliminary results for applying this system to spontaneous facial expressions.