gebhart/patrepeval huggingface dataset:
3D in vitro Models of Pathological Skeletal Muscle: Which Cells and Scaffolds to Elect? (2022)

Skeletal muscle is a fundamental tissue of the human body with great plasticity and adaptation to diseases and injuries. Recreating this tissue <i>in vitro</i> helps not only to deepen its functionality, but also to simulate pathophysiological processes. In this review we discuss the generation of human skeletal muscle three-dimensional (3D) models obtained through tissue engineering approaches. First, we present an overview of the most severe myopathies and the two key players involved: the variety of cells composing skeletal muscle tissue and the different components of its extracellular matrix. Then, we discuss the peculiar characteristics among diverse <i>in vitro</i> models with a specific focus on cell sources, scaffold composition and formulations, and fabrication techniques. To conclude, we highlight the efficacy of 3D models in mimicking patient-specific myopathies, deepening muscle disease mechanisms or investigating possible therapeutic effects.
Neonatal Malrotation with Midgut Volvulus Mimicking Duodenal Atresia (2009)

When the surgical treatment of a patient with the double-bubble sign is to be delayed, an upper gastrointestinal radiographic or ultrasound study is needed to evaluate for malrotation with midgut volvulus.
Abstract 724: Neonatal Heart Regeneration Preserves Native Ventricular Biomechanical Properties After Myocardial Infarction (2019)

Introduction: Neonatal mice exhibit natural heart regeneration after myocardial infarction (MI) until postnatal day 7 (P7). Whether this regenerated muscle is similar biomechanically to native myocardium remains unknown. We hypothesized that neonatal heart regeneration preserves native left ventricular (LV) biomechanical properties after MI. Methods: C57BL/6J mice (n=58) underwent sham surgery or left anterior descending coronary artery ligation on postnatal day 1 (P1) or P7. After 4 weeks, echocardiography was performed. The explanted anterolateral LV wall was mounted for lenticular hydrostatic deformation testing (Fig 1A-B) and pressurized to 130 mmHg with 37°C saline to impart a homogeneous stress load. Surface strain was tracked to calculate a multiaxial composite tissue modulus. Data are expressed as mean±SEM. Results: P1 MI and sham mice (n=14, each) had similar post-MI LV wall thickness (0.61±0.05 cm vs 0.66±0.03 cm, p=0.39), end-diastolic diameter (3.14±0.10 cm vs 3.05±0.12 cm, p=0.57), and ejection fraction (58.2±4.1% vs 55.2±4.4%, p=0.63). P7 MI mice (n=14) had significant LV wall thinning (0.40±0.04 cm vs 0.71±0.02 cm, p&lt;0.0001), end-diastolic LV enlargement (4.24±0.16 cm vs 3.34±0.09 cm, p&lt;0.0001), and depressed ejection fraction (29.7±4.9% vs 61.7±4.0%, p&lt;0.0001) compared to P7 shams (n=16). While LV tissue modulus for P1 MI and sham mice were similar (460.9±46.4 kPa vs 527.1±61.2 kPa, p=0.40, Fig 1C), the modulus for P7 MI mice was significantly elevated compared to that for P7 shams (1099.6±175.1 kPa vs 616.0±95.2 kPa, p=0.02, Fig 1D). Conclusion: In a neonatal mouse MI model, regenerated LV muscle has similar biomechanical properties as native LV muscle.
Acetabular Imprinting Device Improves Accuracy of Component Positioning (2013)

Background: Acetabular component malpositioning in total hip arthroplasty increases the risk of dislocations, impingement, and long-term component wear. The purpose of this Sawbones study was to define the efficacy of a novel acetabular imprinting device (AID) with 3D preoperative planning in accurately placing the acetabular component. Methods: Four surgeons performed the study on osteoarthritic and dysplastic Sawbone models using 3 different methods for placing the acetabular component (total n = 24). The 3 methods included (1) standard preoperative planning and instrumentation (i.e., standard method), (2) 3D computed tomographic (CT) scan planning and standard instrumentation (i.e., 3D planning method), and (3) 3D CT scan planning combined with an acetabular imprinting device (i.e., AID method). In the AID method, 3D planning software was used to virtually place the acetabular component at 40° of inclination and 22° of anteversion and create a parallel guide pin trajectory. A patient-specific surrogate bone model with a built-in guide pin trajectory was then manufactured as a stereoltihography device (Fig. 1A). The surgeon molded bone cement into the acetabulum imprinting the acetabular features while maintaining the guide pin trajectory (Fig. 1B). Afterward, the AID was removed from the surrogate bone model and placed onto the Sawbone, ensuring a secure fit (Fig. 1C). A guide pin was drilled into the Sawbone along the prescribed trajectory. With the guide pin in place, the surgeon could ream the acetabulum and impact the acetabular component using the guide pin as a visual aid (Fig. 1D). Postoperatively, a CT scan was used to define and compare the actual implant location with the preoperative plan. Statistical analysis was performed as 3 group comparisons using the chi-squared test for categorical data and analysis of variance (ANOVA) for continuous measurements. Results: The AID method significantly decreased the mean deviation of acetabular component inclination (3.4°) compared to standard (14.0°) and 3D planning methods (17.4°) (p = 0.003). The mean deviation in version was 10.6° in the standard method, 10.8° in the 3D planning method, and 5.3° in the AID method (p = 0.28). Overall, AID reduced the number of implants malpositioned in excess of 10° from the planned position to 12.5%, compared with 87.5% in the standard method and 75% in the 3D planning method (p = 0.005) (Fig. 2). Conclusions: Novel 3D preoperative planning combined with AID allows the surgeon to accurately replicate the preoperative plan using Sawbones models. This proof-of-concept study justifies a clinical trial to compare the AID to standard surgical techniques.
Hydrogen pressure sensor based on a tapered-FBG written by DUV femtosecond laser technique (2012)

An optical fiber sensor based on a tapered-FBG coated with 150 nm-thick Pd film is proposed for hydrogen pressure detection. The FBG was written in a 50 µm-diameter tapered fiber by DUV femtosecond laser technology. A second FBG was inscribed in the untapered fiber region for temperature compensation. The sensing head was able to detect the variation of hydrogen pressure in the range 0–780 kPa and a maximum sensitivity of 0.15 pm/kPa was achieved.
Catalytic hydrothermal liquefaction of municipal sludge in subcritical water (2021)

In the last decades, the dwindling of the fossil sources of energy coupled with the growth of energy demand and of waste production prompted the research in developing novel industrial technologies for renewable energy production and waste valorization. Hydrothermal liquefaction (HTL) is a good alternative to transform wet biomasses as microalgae, macroalgae, agricultural residues, food waste, and municipal sludge (MS) into value-added products with high efficiency and decreasing the amounts that has to be disposed of. HTL takes place in an aqueous environment, without the energy cost of drying the biomass, at 300-400°C and pressure of 10-40 MPa [1,2]. At these operative conditions, an integral degradation of wet biomass produces a bio-oil termed biocrude and other C-containing products i.e. a solid residue, a gaseous phase rich in CO2 and an aqueous phase with soluble organics. The development of the process to the industrial scale is hindered by many challenges related both to the heterogeneous nature of the raw material and the complexity of the phase behavior downstream of the process and the poor quality of the biocrude produced as fuel precursor. This work aims to investigate the potentiality of catalytic HTL to obtain a biocrude more competitive as fuel precursor. We have studied catalytic HTL of MS in a stirred AISI 316 high-pressure batch reactors at 325 °C and 30 min as reaction temperature and time using NiMo/Al2O3, CoMo/Al2O3 and activated carbon felt as catalysts and formic acid (FA) as liquid hydrogen donor. Optimized work-out procedures were used to separate and quantify the products with the aim to decrease the amount of not detected mass [3]. With adopted methods the formation of an hydrocarbon fraction (HC) recovered from the biocrude, was detected in the presence of the catalysts. This result indicates that tested catalysts promote the in-situ up-grading of the produced biocrude. Furthermore, the addition of FA as liquid hydrogen donor allowed us to achieve higher H/C and HHV of biocrude as it was possible to increase the biocrude yield at more than 50% with energy recovery approaching 100%. Collected results suggest that use of catalysts can increase the yield and quality of biocrude in the HTL of municipal sludge.
Heterogeneity of CD4+ memory T cells: Functional modules for tailored immunity (2009)

Phenotypic and functional heterogeneity is the hallmark of effector and memory T cells. Upon antigenic stimulation, naïve CD4(+) T cells make choices to become effector Th1, Th2 or Th17 cells, or even Treg. In addition to differences in cytokine repertoire, effector CD4(+) T cells exhibit diversity in homing, such as migration to lymph node follicles to help B cells versus migration to inflamed tissues. Upon clearance of the antigen, two major types of memory T cells remain: central memory cells, which patrol lymphoid organs, and effector memory cells that act as sentinels in peripheral tissues such as the skin and the gut. Here, we review our current understanding of CD4(+) T-cell lineage heterogeneity and flexibility, with emphasis on the human system, and propose an organization of effector and memory T cells based on distinct functional modules.
Modified Intervention-Less Inflow Control Device for Water Management (2016)

Abstract Excessive water production shortens the life of producing wells and severely limits their economic viability. Inflow control devices (ICDs) are used to halt water output and compensate for permeability variation by shutting off the sleeve where water production increases. Traditional ICDs need activation and intervention for the water shut-off, which leads to non-productive time, increased cost, and reduced revenue. Intervention-less passive technology addresses this imbalance issue by designing an ICD that highly reduces water breakthrough into the wellbore in virtually any porous media. The intelligent well completion technology presented in this paper focuses on a modified ICD with no movable parts for water management. The ICD annulus is packed with a porous Polytetrafluoroetheylene (PTFE) sleeve that exhibits water-sensitive control functions. The porous PTFE sleeve causes a differential pressure for water and oil through the modified ICD. Differential pressure occurs because hydrophobic material and brine form droplets due to their higher surface tension, whereas oil flows in a more streamline manner. This situation leads to choking of the pore throat and higher pressure in the flow loop for higher brine cut. Flow testing through porous a PTFE sleeve shows about 200 % increase in differential pressures for 70% brine cuts compared to 0% water cut, which means it can restrict flow when the brine cut increases. The porous PTFE material has high thermal and chemical stability and can tolerate salinities as high as 246,000 ppm for long periods of time. Tests have confirmed the efficacy of the tool remains unchanged, even after flowing brine and diesel through the material for more than 400 hours. Prototype testing indicates that the modified ICD significantly improves recovery performance. This innovative tool will be field tested shortly. This modified inflow control device offers a novel intervention-less, reversible subsurface water management technology by reducing production from zones with high water cuts.
Effects of polarization in low-level laser therapy of spinal cord injury in rats (2012)

Low-level laser therapy (LLLT) is a promising approach to treat the spinal cord injury (SCI). Since nerve fibers have optical anisotropy, propagation of light in the spinal tissue might be affected by its polarization direction. However, the effect of polarization on the efficacy of LLLT has not been elucidated. In the present study, we investigated the effect of polarization on the efficacy of near-infrared LLLT for SCI. Rat spinal cord was injured with a weight-drop device. The lesion site was irradiated with an 808-nm diode laser beam that was transmitted through a polarizing filter immediately after injury and daily for five consecutive days. The laser power at the injured spinal cord surface was 25 mW, and the dosage per day was 9.6 J/cm2 (spot diameter, 2 cm; irradiation duration, 1200 s). Functional recovery was assessed daily by an open-field test. The results showed that the functional scores of the SCI rats that were treated with 808-nm laser irradiation were significantly higher than those of the SCI alone group (Group 1) from day 5 after injury, regardless of the polarization direction. Importantly, as compared to the locomotive function of the SCI rats that were treated with the perpendicularly-polarized laser parallel to the spinal column (Group 2), that of the SCI rats that were irradiated with the linearly aligned polarization (Group 3) was significantly improved from day 10 after injury. In addition, the ATP contents in the injured spinal tissue of Group 3, which were measured immediately after laser irradiation, were moderately higher than those of Group 2. These observations are attributable to the deeper penetration of the parallelpolarized light in the anisotropic spinal tissue, suggesting that polarization direction significantly affects the efficacy of LLLT for SCI.
Information extraction meets relation databases (2009)

Information extraction from unstructured text has much in common with querying in databases systems. Despite some differences on how data is modeled or represented, the general goal remains the same, i.e. to retrieve data or tag elements that satisfy some user-specified constraints. In recent years, the two paradigms have become much closer thanks to the large volume of data on the World Wide Web and the need for more automated search tools for information extraction and often the need for relating the extracted pieces. Several developments have contributed to the growth of the area including the work on named entity recognition (marked by MUC-6 and subsequent conferences) and natural language processing, Web information retrieval and mining, and Web query languages inspired by the query languages in the relational world. This panel explores the areas where the two paradigms overlap, the impacts and contributions they have had on each other and the areas that may be open for further research. The panel will bring together researchers who have worked in some established areas that closely relate to extracting structured information from unstructured text. In the first (role-playing) round, each panelist will strongly take a side on where the intersection is heading, arguing that one area will subsume the other area in near future. In the second round, the panelists will counter one or two others, pointing out the challenges that one area would be facing in subsuming the other and implications for future research directions.
Supplemental Figure 1 from Toll-like Receptor Agonist Imiquimod Facilitates Antigen-Specific CD8<sup>+</sup> T-cell Accumulation in the Genital Tract Leading to Tumor Control through IFNγ (2023)

&lt;p&gt;Supplemental Figure 1. E7-specific T cells efficiently migrated from circulation to the genital tract following imiquimod application&lt;/p&gt;
Supplementary Fig S4 from Gemcitabine Mechanism of Action Confounds Early Assessment of Treatment Response by 3′-Deoxy-3′-[<sup>18</sup>F]Fluorothymidine in Preclinical Models of Lung Cancer (2023)

&lt;p&gt;Gemcitabine induces increased apoptosis in H1975 tumors on d5.&lt;/p&gt;
DETECTION AND CLASSIFICATION OF CHALLENGING TARGETS (2013)

Discrimination of challenging targets, such as small and deep targets in highly cluttered environments, is still an enormous problem for UXO industry. Advanced electromagnetic induction (EMI) sensors currently feature multi-axis illumination of targets and tri-axial vector sensing (e.g., MetalMapper), or exploit multi-static array data acquisition (e.g., TEMTADS). They produce data of high density, quality, and diversity, and have been combined with advanced EMI models to provide superb classification performance relative to the previous generation of single-axis, monostatic sensors. However, these advances yet have to improve significantly our ability to classify challenging targets, such as small and deep targets, or provide the high fidelity necessary to distinguish overlapping target signatures in highly cluttered environments. The objective of this paper is to develop fast, noise-tolerant EMI data pre-processing approaches and improve the detection limits of current sensors, thus bringing our advanced EMI models and classification algorithms to the next level of complexity that will enable the discrimination of small and deep targets. Namely, we will illustrate a combined software and hardware approach that will provide extended detection range and spatial resolution of next-generation EMI systems; will illustrate a fast target-discrimination algorithm based on the static response matrix eigenvalues’ time-decay patterns in a real time, and will demonstrate the Multi-Signal Characteristic (MUSIC) algorithm to infer target locations from the actual TEMTADS data sets. In addition, the advanced models classification performance will be compare to the traditional simple dipole model approach for a small and deeply buried 20 mm projectile's Metal Mapper data set
Thermally enhanced blue light-emitting diode (2015)

We investigate thermoelectric pumping in wide-bandgap GaN based light-emitting diodes (LEDs) to take advantage of high junction temperature rather than avoiding the problem of temperature-induced efficiency droop through external cooling. We experimentally demonstrate a thermally enhanced 450 nm GaN LED, in which nearly fourfold light output power is achieved at 615 K (compared to 295 K room temperature operation), with nearly no reduction in the wall-plug efficiency (i.e., electrical-optical energy conversion efficiency) at bias V&amp;lt;ℏω/q. The LED is shown to work in a mode similar to a thermodynamic heat engine operating with charged carriers pumped into the active region by a combination of electrical work and Peltier heat (phonons) drawn from the lattice. In this optimal operating regime at 615 K, the LED injection current (3.26 A/cm2) is of similar magnitude to the operating point of common high power GaN based LEDs (5–35 A/cm2). This result suggests the possibility of removing bulky heat sinks in current high power LED products thus realizing a significant cost reduction for solid-state lighting.
Purification and regulation of CTP:phosphocholine cytidylyltransferase (2010)

CTP:phosphocholine cytidylyltransferase was purified to homogeneity using a procedure involving aggregation of enzyme with exogenous lipid and selective dissociation with detergents and chromatography on conventional and FPLC columns. SDS-PAGE of purified enzyme showed a single protein of molecular weight ~42 Kd. Native-PAGE showed the protein to migrate at a molecular weight of ~90 Kd, indicating that the native enzyme may be a dimer. IEF-PAGE revealed the enzyme to have a pI of ~5.8. 2-D-PAGE showed the enzyme to have at least two isoforms. Attempts to generate polyclonal antibody to the purified enzyme in rabbits were unsucessful. Even after two booster injections, the antibody titre was still weak indicating that the enzyme may not be a good antigen. However, Dr Harris Jamil was able to generate antibodies in the chicken. This antibody detected cytidylyltransferase by the Western-blotting technique and inhibited enzyme activity in a concentration-dependent manner, but was unable to immunoprecipitate the cytidylyltransferase in solution. Using this antibody, the cytidylyltransferase was found to occur in a variety of isoforms. Kinetic studies using the purified enzyme showed the K[sub m] for CTP and phosphocholine to be 0.31 mM and 0.15 mM respectively. Activation of cytidylyltransferase by commercial and microsomal lipids showed the enzyme to be activated by anionic phospholipids. The presence of oleate did not greatly enhance the activation of the enzyme by these lipids. The purified cytidylyltransferase was shown to be a substrate for cAMP-dependent protein kinase. Phosphorylation of the enzyme led to inactivation and increased recovery of the enzyme in the cytosol, while dephosphorylation by alkaline phosphatase led to activation and increased recovery of the enzyme in the microsomes. A serine residue(s) was phosphorylated on cytidylyltransferase. Twice as much phosphate was incorporated if cytidylyltransferase were dephosphorylated prior to phosphorylation. Incubation of hepatocytes with ³²Pi and then detection of cytidylyltransferase with antibody after 2-D-PAGE and Western-blotting, showed the cytidylyltransferase may be phosphorylated in vivo. Incubation of hepatocytes with Ca²⁺, Ca²⁺-mobilizing agents and phospholipase A₂ resulted in translocation of cytidylyltransferase from the cytosol to the microsomes. Incubation of hepatocytes with Ca²⁺ resulted in an increase in PC and LPC formation. Incubation of hepatocytes with phospholipase A₂ resulted in an increase in PC formation. Regulation of cytidylyltransferase activity by reversible phosphorylation and by Ca²⁺ may be important during short term regulation of enzyme activity by hormones.
Silica Nanostructures Produced Using Diatom Peptides with Designed Post‐Translational Modifications (2020)

Abstract Diatoms produce intricately patterned silica structures under ambient conditions, a process initiated by post‐translationally modified silaffin peptides that nucleate silicic acid. Designing these peptides would enable the production of silica nanostructures with desired properties; however, the functional effects of modifications are poorly understood. Here, Escherichia coli is used to express and modify recombinant silaffin R5 peptide from the diatom Cylindrotheca fusiformis . A library of 38 enzymes is tested for R5 modifications in vitro, from which active methyltransferases, kinases, acetyltransferases, oxidases, and myristoyltransferases are identified from diatoms, humans, yeast, and bacteria. Modified R5 peptides are used for silica precipitation and the impacts on particle size, shape, porosity, and surface area are quantified. In vivo pathways are designed to coexpress R5 and a modifying enzyme and the resulting peptide is used to nucleate silica nanostructures with controlled size (100–3500 nm), porosity (20–635 m 2 g −1 ), or embedded with melanin. It is found that phosphorylation reduces the need for inorganic phosphate during silica synthesis. The simultaneous methylation and phosphorylation of R5 leads to smaller particles requiring less inorganic phosphate. Inspired by diatoms, the use of post‐translationally modified peptides will enable the control of silica morphology under ambient conditions, with potential applications in electronics and photonics.
Baseline extended zone retinal vascular calibres associate with sensory nerve abnormalities in adolescents with type 1 diabetes: A prospective longitudinal study (2021)

Narrower extended zone retinal calibres were associated with sensory nerve abnormality in adolescents with type 1 diabetes and may present useful biomarkers to understand the pathophysiology of neuropathy.