gebhart/patrepeval huggingface dataset:
Biological approaches to improve skeletal muscle healing after injury and disease (2012)

Skeletal muscle injury and repair are complex processes, including well-coordinated steps of degeneration, inflammation, regeneration, and fibrosis. We have reviewed the recent literature including studies by our group that describe how to modulate the processes of skeletal muscle repair and regeneration. Antiinflammatory drugs that target cyclooxygenase-2 were found to hamper the skeletal muscle repair process. Muscle regeneration phase can be aided by growth factors, including insulin-like growth factor-1 and nerve growth factor, but these factors are typically short-lived, and thus more effective methods of delivery are needed. Skeletal muscle damage caused by traumatic injury or genetic diseases can benefit from cell therapy; however, the majority of transplanted muscle cells (myoblasts) are unable to survive the immune response and hypoxic conditions. Our group has isolated neonatal skeletal muscle derived stem cells (MDSCs) that appear to repair muscle tissue in a more effective manner than myoblasts, most likely due to their better resistance to oxidative stress. Enhancing antioxidant levels of MDSCs led to improved regenerative potential. It is becoming increasingly clear that stem cells tissue repair by direct differentiation and paracrine effects leading to neovascularization of injured site and chemoattraction of host cells. The factors invoked in paracrine action are still under investigation. Our group has found that angiotensin II receptor blocker (losartan) significantly reduces fibrotic tissue formation and improves repair of murine injured muscle. Based on these data, we have conducted a case study on two hamstring injury patients and found that losartan treatment was well tolerated and possibly improved recovery time. We believe this medication holds great promise to optimize muscle repair in humans.
Use of Oleogels to Replace Margarine in Steamed and Baked Buns (2021)

Bakery products are usually formulated with solid fats, like margarines and shortenings, which contain high levels of saturated and trans-fatty acids and have negative effects on human health. In this study, hydroxypropyl methylcellulose (HPMC) and xanthan gum (XG) were used as oleogelators to prepare oleogels, using sunflower and olive oil, as substitutes for margarine in baked or steamed buns. The effect of oleogels on the physical properties of the buns was evaluated by analyzing the crumb structure, specific volume, height, and texture. In addition, a triangular discriminatory sensory test was conducted, and lipid digestibility was assessed through in vitro digestion studies. Replacement of margarine with oleogels produced steamed buns with no differences in the crumb structure, volume, height, and texture; however, in baked buns, a less porous and harder structure was produced. No differences in texture were observed between the margarine buns and buns made with oleogels when the triangular test was conducted. The extent of lipolysis was not affected when margarine was replaced by oleogels in the baked and steamed buns. The results suggest that using oleogels instead of margarine in buns could represent an interesting strategy to prepare healthier bakery products.
Linfonodo sentinela intramamário comprometido e axila livre: esvaziamento axilar ou conduta conservadora? (2012)

The sentinel lymph node biopsy is a standard treatment for patients with breast cancer and clinically negative axilla lymph node. The presence of an extra-axillary and intra-axillary (IM) sentinel lymph node (SLN) occurs in up to 2.6% of cases. In the presence of a metastatic IM SLN, axillary positivity may occur in up to 81% of cases. Due to the limited number of cases reported, there is no standard treatment for the association of metastatic SLN IM and non-metastatic axillary SLN . We add here two cases to the literature, one of them with metastatic disease in the axilla. The use of a nomogram demonstrated that the risk of axillary metastasis was less than 10% and the addition of these cases to the literature showed that in this situation the rate of axillary metastasis is 6.25%. We discuss the pros and cons of further axillary dissection in this situation.
Supplementary Data from Rare but Recurrent ROS1 Fusions Resulting From Chromosome 6q22 Microdeletions are Targetable Oncogenes in Glioma (2023)

&lt;p&gt;Supplementary Figures&lt;/p&gt;
d-Glycerate Transport by the Pea Chloroplast Glycolate Carrier (1986)

The transport of glycolate and d-glycerate, the substrate and end product of the photorespiratory carbon pathway, respectively, by isolated intact pea (Pisum sativum) chloroplasts has been compared. d-Glycerate uptake was inhibited by the 2-hydroxymonocarboxylates, glycolate, glyoxylate, and d-lactate. Phosphate and phosphoglycerate and triose phosphates were without effect when the assays were carried out for two seconds. Glycolate was found to be a competitive inhibitor of d-glycerate uptake and the presence of glycolate in the chloroplast stroma strongly enhanced d-glycerate uptake from the medium. For optimal rates of d-glycerate-dependent O(2) evolution by pea chloroplasts, phosphate, ADP or ATP, and a mediator of cyclic electron flow had to be added. The inhibition of d-glycerate-dependent O(2) evolution by triose phosphates and 2-hydroxymonocarboxylates was tested. The inhibition of d-glycerate-dependent O(2) evolution by these metabolites did not correlate with their effects on glycerate transport. Thus, metabolism of d-glycerate, rather than its transport, limits the rate of glycerate-dependent oxygen evolution. The ramifications of d-glycerate metabolism on the interpretation of d-glycerate uptake data obtained with prolonged incubations are discussed. We conclude that d-glycerate and glycolate transport are mediated by the same transport system.
Iterative Frequency Domain Equalization and Carrier Synchronization for Multi-Resolution Constellations (2010)

Broadband broadcast and multicast wireless systems usually employ OFDM modulations (Orthogonal Frequency Division Multiplexing) combined with non-uniform hierarchical constellations. However, these schemes are very prone to nonlinear distortion effects and have high carrier synchronization requirements. SC-FDE (Single-Carrier with Frequency-Domain Equalization) is an attractive alternative for OFDM, especially when an efficient power amplification is intended. In this paper we consider the use of SC-FDE schemes combined with non-uniform hierarchical constellations in broadband broadcast and multicast wireless systems. We study the impact of residual CFO (Carrier Frequency Offset) on the performance of multi-resolution schemes and we propose iterative frequency domain receivers with joint detection and carrier synchronization to cope with residual CFO estimation errors (a coarse CFO estimation and compensation is assumed before the equalization procedure). Our results show that while a very high carrier synchronization accuracy is required for the least protected bits, the most protected bits are relatively robust to the CFO. By employing the proposed receiver we increase significantly the robustness to residual CFO estimation errors.
Reliable computation of the eigenvalues of the discrete KdV spectrum (2022)

We propose a numerical algorithm that computes the eigenvalues of the Korteweg–de Vries equation (KdV) from sampled input data with vanishing boundary conditions. It can be used as part of the Non-linear Fourier Transform (NFT) for the KdV equation. The algorithm that we propose makes use of Sturm Liouville (SL) oscillation theory to guaranty that all eigenvalues are found. In comparison to similar available algorithms, we show that our algorithm is more robust to numerical errors and thus more reliable. Furthermore we show that our root finding algorithm, which is based on the Newton–Raphson (NR) algorithm, typically saves computation time compared to the conventional approaches that rely heavily on bisection.
Data from Targeted Inhibition of Cyclic AMP Phosphodiesterase-4 Promotes Brain Tumor Regression (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; As favorable outcomes from malignant brain tumors remain limited by poor survival and treatment-related toxicity, novel approaches to cure are essential. Previously, we identified the cyclic AMP phosphodiesterase-4 (PDE4) inhibitor Rolipram as a potent antitumor agent. Here, we investigate the role of PDE4 in brain tumors and examine the utility of PDE4 as a therapeutic target.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Immunohistochemistry was used to evaluate the expression pattern of a subfamily of PDE4, PDE4A, in multiple brain tumor types. To evaluate the effect of PDE4A on growth, a brain-specific isoform, PDE4A1 was overexpressed in xenografts of Daoy medulloblastoma and U87 glioblastoma cells. To determine therapeutic potential of PDE4 inhibition, Rolipram, temozolomide, and radiation were tested alone and in combination on mice bearing intracranial U87 xenografts.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We found that PDE4A is expressed in medulloblastoma, glioblastoma, oligodendroglioma, ependymoma, and meningioma. Moreover, when PDE4A1 was overexpressed in Daoy medulloblastoma and U87 glioblastoma cells, &lt;i&gt;in vivo&lt;/i&gt; doubling times were significantly shorter for PDE4A1-overexpressing xenografts compared with controls. In long-term survival and bioluminescence studies, Rolipram in combination with first-line therapy for malignant gliomas (temozolomide and conformal radiation therapy) enhanced the survival of mice bearing intracranial xenografts of U87 glioblastoma cells. Bioluminescence imaging indicated that whereas temozolomide and radiation therapy arrested intracranial tumor growth, the addition of Rolipram to this regimen resulted in tumor regression.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This study shows that PDE4 is widely expressed in brain tumors and promotes their growth and that inhibition with Rolipram overcomes tumor resistance and mediates tumor regression.&lt;/p&gt;&lt;/div&gt;
Model of Intraperitoneal Targeted α-Particle Therapy Shows That Posttherapy Cold-Antibody Boost Enhances Microtumor Radiation Dose and Treatable Tumor Sizes (2017)

Intraperitoneally administered radiolabeled monoclonal antibodies (mAbs) have been tested in several clinical trials, often with promising results, but have never proven curative. <b>Methods:</b> We have previously presented simulations of clinically relevant amounts of intraperitoneal <sup>90</sup>Y-mAbs for treatment of minimal disease and shown that such treatments are unlikely to eradicate microtumors. Our previous model simulated the kinetics of intraperitoneally infused radiolabeled mAbs in humans and showed the benefit of instead using α-emitters such as <sup>211</sup>At. In the current work, we introduce penetration of mAbs into microtumors with radii of up to 400 μm. Calculations were performed using dynamic simulation software. To determine the radiation dose distribution in nonvascularized microtumors of various sizes after intraperitoneal <sup>211</sup>At-radioimmunotherapy, we used an in-house-developed Monte Carlo program for microdosimetry. Our aim was to find methods that optimize the therapy for as wide a tumor size range as possible. <b>Results:</b> Our results show that high-specific-activity radiolabeled mAbs that are bound to a tumor surface will penetrate slowly compared with the half-lives of <sup>211</sup>At and shorter-lived radionuclides. The inner-core cells of tumors with radii exceeding 100 μm may therefore not be sufficiently irradiated. For lower specific activities, the penetration rate and dose distribution will be more favorable for such tumors, but the dose to smaller microtumors and single cells will be low. <b>Conclusion:</b> Our calculations show that the addition of a boost with unlabeled mAb 1-5 h after therapy results in sufficient absorbed doses both to single cells and throughout microtumors up to approximately 300 μm in radius. This finding should also hold for other high-affinity mAbs and short-lived α-emitters.
Timeloop: A Systematic Approach to DNN Accelerator Evaluation (2019)

This paper presents Timeloop, an infrastructure for evaluating and exploring the architecture design space of deep neural network (DNN) accelerators. Timeloop uses a concise and unified representation of the key architecture and implementation attributes of DNN accelerators to describe a broad space of hardware topologies. It can then emulate those topologies to generate an accurate projection of performance and energy efficiency for a DNN workload through a mapper that finds the best way to schedule operations and stage data on the specified architecture. This enables fair comparisons across different architectures and makes DNN accelerator design more systematic. This paper describes Timeloop's underlying models and algorithms in detail and shows results from case studies enabled by Timeloop, which provide interesting insights into the current state of DNN architecture design. In particular, they reveal that dataflow and memory hierarchy co-design plays a critical role in optimizing energy efficiency. Also, there is currently still not a single architecture that achieves the best performance and energy efficiency across a diverse set of workloads due to flexibility and efficiency trade-offs. These results provide inspiration into possible directions for DNN accelerator research.
Hematopoietic Stem Cell Transplantation in CSF1R-Related Leukoencephalopathy: Retrospective Study on Predictors of Outcomes (2022)

Mutations in the <i>CSF1R</i> gene are the most common cause of adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP), a neurodegenerative disease with rapid progression and ominous prognosis. Hematopoietic stem cell transplantation (HSCT) has been increasingly offered to patients with <i>CSF1R</i>-ALSP. However, different therapy results were observed, and it was not elucidated which patient should be referred for HSCT. This study aimed to determine predictors of good and bad HSCT outcomes in <i>CSF1R</i>-ALSP. We retrospectively analyzed 15 patients, 14 symptomatic and 1 asymptomatic, with <i>CSF1R</i>-ALSP that underwent HSCT. Median age of onset was 39 years, and the median age of HSCT was 43 years. Cognitive impairment was the most frequent initial manifestation (43%), followed by gait problems (21%) and neuropsychiatric symptoms (21%). Median post-HSCT follow-up was 26 months. Good outcomes were associated with gait problems as initial (<i>p</i> = 0.041) and predominant (<i>p</i> = 0.017) manifestation and younger age at HSCT (<i>p</i> = 0.044). Cognitive impairment as first manifestation was a predictor of a bad outcome (<i>p</i> = 0.016) and worsening of cognition post-HSCT (<i>p</i> = 0.025). In conclusion, gait problems indicated a milder phenotype with better response to HSCT and good therapy outcomes. In contrast, patients with a higher burden of cognitive symptoms were most likely not to benefit from HSCT.
Generation of F centres and hole centres in the nonstoichiometric x-ray storage phosphor BaFBr (1998)

After x-irradiation of nonstoichiometric , besides the centre a new intrinsic hole centre was found by electron paramagnetic resonance (EPR). The powder EPR line of this new centre can be simulated assuming an molecule on a fluoride site. The new hole centre is stable at room temperature and is the anti-centre of the centre in the F centre generation process. Magic angle spinning nuclear magnetic resonance (MAS-NMR) experiments on nonstoichiometric show not only resonances of on regular lattice sites, but also resonances which are due to on bromine sites (`fluorine antisites'). There are about 10% fluorine antisites in the nonstoichiometric powder which corresponds to the excess fluorine determined by chemical analysis. The generation of electron trap-hole trap pairs upon x-irradiation originates at the fluorine antisites.
ASDM Clinical Case Focus: Persistent Left Superior Vena Cava: Diagnosis and Implications for the Interventional Nephrologist (2006)

Awareness and recognition of anatomic anomalies of the great vessels of the neck and chest are important for the interventional nephrologist, as central venous catheter placement is a common procedure. A persistent left superior vena cava (PLSVC) is the most common thoracic venous anomaly (0.3-0.5% of the population), and can present difficulty during internal jugular or subclavian vein catheter insertion, as well as pose a diagnostic dilemma. In this report, two cases of PLSVC are described, and the clinical significance and diagnosis of PLSVC are reviewed.
Differential Expression of Activator Protein-1 Transcription Factors in Pregnant Rat Myometrium1 (2002)

While the AP-1 (activator protein-1) genes c-fos and c-jun have been implicated in the expression of myometrial genes associated with the onset of labor, there are no data concerning the role of other members of this family of transcription factors. To address this issue, we defined the expression and hormonal regulation of AP-1 genes in the rat myometrium during pregnancy and labor. Tissue was collected on Days 12, 15, 17, 19, 21, 22, and 23 (labor) and 1 day postpartum. Expression of c-fos, fosB, fra-1, fra-2, and junB was low during early gestation, with a 5- to 10-fold increase on Day 23 during labor, and returned to low levels 1 day postpartum. In contrast, the levels of c-jun and junD remained relatively constant throughout gestation. Administration of progesterone (P4; 16 mg/kg s.c./day) beginning on Day 20 (to maintain elevated plasma P4 levels) prevented the onset of labor and blocked the expected rise in c-fos, fosB, fra-1, fra-2, and junB expression on Day 23. In contrast, administration of the progesterone receptor antagonist RU486 (10 mg/kg s.c.) on Day 19 induced preterm labor and a premature increase in mRNA levels of c-fos, fra-1, fra-2, and junB. In unilaterally pregnant rats, stretch imposed by the growing fetus was found to increase the expression of c-fos, fosB, fra-1, fra-2, and junB only in the gravid horn on the day of labor. These data raise the possibility that AP-1 transcription factors integrate endocrine and mechanical signals, leading to myometrial gene expression required for uterine remodeling and the initiation of labor.
Competitive surface-enhanced Raman scattering assay for the 1,25-dihydroxy metabolite of vitamin D3 (2010)

This paper describes the development and preliminary testing of a competitive surface-enhanced Raman scattering (SERS) immunoassay for calcitriol, the 1,25-dihydroxy metabolite (1,25-(OH)2-D3) of vitamin D3. Deficiencies in 1,25-(OH)2-D have been linked to renal disease, while elevations are linked to hypercalcemia. Thus, there has been a sharp increase in the clinical demand for measurements of this metabolite. The work herein extends the many attributes of SERS-based sandwich immunoassays that have been exploited extensively in the detection of large biolytes (e.g., DNA, proteins, viruses, and microorganisms) into a competitive immunoassay for the low level determination of a small biolyte, 1,25-(OH)2-D3 (Mw = 416 g mol−1). The assay uses surface modified gold nanoparticles as SERS labels, and has a dynamic range of 10–200 pg mL−1 and a limit of detection of 8.4 ± 1.8 pg mL−1. These analytical performance metrics match those of tests for 1,25-(OH)2-D3 that rely on radio- or enzyme-labels, while using a much smaller sample volume and eliminating the disposal of radioactive wastes. Moreover, the SERS-based data from pooled-patient sera show strong agreement with that from radioimmunoassays. The merits and potential utility of this new assay are briefly discussed.
An efficient pipelined dataflow processor architecture (1988)

This paper demonstrates that the principles of pipelined instruction execution can be effectively applied in dataflow computers, yielding an architecture that avoids the main sources of pipeline gaps during program execution in many conventional processor designs. The new processing element design uses an architecture called argument-fetch dataflow architecture. It has two parts: a dataflow instruction scheduling unit (DISU) and a pipelined instruction processing unit (PIPU). The PIPU is an instruction processor that uses many conventional techniques to achieve fast pipelined operation. The DISU holds the dataflow signal graph of the collection of dataflow instructions allocated to the processing element, and maintains a large pool of enabled instructions available for execution by the PIPU. The new architecture provides a basis for achieving high performance for many scientific applications. To show that the realization of an efficient dataflow processing element is feasible, a trial design and fabrication of an enable memory-a key component of the DISU-is reported.
Quantitative Determination of Saccharides in Dietary Glyconutritional Products by Anion-Exchange Liquid Chromatography with Integrated Pulsed Amperometric Detection (2005)

A new technique for the assay of carbohydrates is described in which separation and quantification of neutral saccharides, aminosaccharides, glycuronic acids, and disaccharides may be accomplished in less than 50 min of total run time. This method involves optimized anion-exchange liquid chromatography coupled with integrated pulse amperometric detection. Complex carbohydrates from various sources, including dietary supplements, were hydrolyzed in a dilute solution of trifluoroacetic acid, freeze-dried, and reconstituted in water containing 2-deoxygalactose as the internal standard. The solution was filtered and separated on CarboPac PA20 column. The eluted saccharides were detected by oxidation on a gold electrode with quadruple-pulsed integrated amperometry. The calibration plots for the saccharides were linear with an average correlation coefficient of 0.999. Method precision regarding peak retention time and resolution used in the peak identifications was verified. With this method, previously difficult-to-separate saccharides, such as galactosamine, glucosamine, and N-acetylglucosamine, were successfully resolved from the neutral saccharides rhamnose, arabinose, and galactose. Mannose was also resolved from xylose, and de-acetylation of aminosaccharides prior to separation was not necessary. This technique provides an accurate and efficient means to assay carbohydrates in dietary supplements, which new federal regulations will soon mandate.
Hybrid Monte Carlo filtering: edge-based people tracking (2003)

Statistical inefficiency often limits the effectiveness of particle filters for high-dimensional Bayesian tracking problems. To improve sampling efficiency on continuous domains, we propose the use of a particle filter with hybrid Monte Carlo (HMC), an MCMC (Markov chain Monte Carlo) method that follows posterior gradients toward. high probability states, while ensuring a properly weighted approximation to the posterior. We use HMC filtering to infer the 3D shape and motion of people from natural, monocular image sequences. The approach currently uses an empirical, edge-based likelihood function, and a second-order dynamic model with soft biomechanical joint constraints.