gebhart/patrepeval huggingface dataset:
Principles and Practices of Unbiased Stereology: An Introduction for Bioscientists (2002)

Contents: Preface Introduction 1 The History of Stereology 2 Bias 3 Sampling 4 Geometric Probes 5 Bias in Estimating Number 6 The Disector Principle 7 Volume 8 Length and Surface Area 9 Nonstereological Bias 10 All Variation Considered 11 Typical Stereology Designs 12 Frequent Questions about Stereology Appendix. Conceptual Framework of Modern Stereology Glossary Bibliography Index
Morphological and steroidogenic changes in cultured adrenal tumor cells induced by a subunit of cholera enterotoxin (1976)

A purified subunit of the cholera enterotoxin molecule was found to have morphological and steroidogenic inducing effects similar to those induced by the native enterotoxin on monolayer tissue cultures of Y1 adrenal tumor cells, although 1,000 times more subunit than toxin (weight basis) was required for maximal effects. In contrast to the whole toxin, the effects of the active subunit could not be prevented by prior incubation with either Gm1 ganglioside or with antibodies directed against choleragenoid (the binding subunit). These results suggest that different receptor sites may exist on cells for the binding and for the active subunits of cholera enterotoxin and/or that the active toxin fragment may exert its effects after gaining access to the intracellular compartment.
Impact of graft‐versus‐host disease and graft‐versus‐leukemia effect based on minimal residual disease in Philadelphia chromosome‐positive acute lymphoblastic leukemia (2020)

The impacts of graft-versus-host disease (GVHD) and graft-versus-leukemia (GVL) effect might differ depending on minimal residual disease (MRD). Therefore, we examined 1,022 recipients who underwent their first allogeneic hematopoietic stem cell transplantation (HSCT) for Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph-positive ALL) in first complete remission. MRD status at HSCT was negative in 791 (77·4%) and positive in 231 (22·6%). The impact of GVHD as a time-dependent covariate on transplant outcomes were analyzed while adjusting for other possible variables. Mild acute GVHD [hazard ratio (HR), 0·90; 95% confidence interval (CI), 0·70-1·16; P = 0·901] and chronic GVHD (HR, 0·82, 95% CI, 0·58-1·14; P = 0·238) were not significantly associated with overall mortality, whereas severe acute GVHD (HR, 2·26, 95% CI, 1·64-3·11; P < 0·001) resulted in inferior overall survival due to high non-relapse mortality. Moreover, even in the subgroup analyses stratified according to MRD status, acute and chronic GVHD were not significantly associated with better overall survival. Therefore, less intensive GVHD prophylaxis to achieve a GVL effect is not recommended for Ph-positive ALL.
Microsensors and microactuators using ferroelectric thin films (2002)

Various microsensor and microactuators using ferroelectric thin films such as infrared sensors, ultrasonic sensors, piezoelectric actuators and optical switches have been reviewed with the other electronic devices of semiconductor memories and electroluminescent device with low-threshold voltage. A series or technical data for preparing ferroelectric thin films such as PbTiO/sub 3/, PZT, PLZT and BST by using various methods such as RF sputtering, laser ablation, chemical vapor deposition and the sol-gel method are described. The obtained thin films show very good ferroelectric, pyroelectric, piezoelectric and electro-optic properties.
Screening for Sepsis: A Key Strategy for Early Identification and Management of Septic Patients (2014)

Background: Sepsis, defined as a systemic inflammatory response to infection, is a life-threatening medical condition that rapidly progresses from severe sepsis (characterized by signs of organ dysfunction) to septic shock with fluid-refractory hypotension. Adherence to the Surviving Sepsis Campaign guidelines for the management of severe sepsis and septic shock have been associated with improved delivery of care and reduced mortality. Delays in recognition of sepsis has been identified as a barrier to achieving early goal-directed therapy targets. Purpose: To determine if a sepsis screening protocol could facilitate earlier identification of patients with sepsis Methods: A retrospective medical record review was conducted for adult patients with a primary or secondary diagnosis of sepsis using ICD-9 codes 038.9 (unspecified septicemia), 995.91 (sepsis), 995.92 (severe sepsis), and 785.52 (septic shock). A sepsis screening strategy was applied retrospectively to simulate implementation of a screening protocol. Application of the screening strategy was performed to quantify the interval between when clinicians first recognized sepsis and when patients first exhibited signs of systemic inflammatory response syndrome (SIRS). Results: The median interval of time between when a clinician recognized sepsis and when a patient first exhibited signs of sepsis was 222 minutes. A difference in time occurred in 22% of the cases. Duration of the interval was positively correlated with hospital length of stay (rs = .65, n = 17, p = .005). Conclusion: The interval between when patients with sepsis were first identified by a clinician (without screening) and when those patients could have been recognized utilizing a screening protocol was quantified. Results suggest that more than one in five patients would have been identified earlier using a screening protocol. A pilot study to further investigate the potential impact of sepsis screening on time to identification is warranted.
Review: The unhappy chaperone — R1/PR5 (2021)

Chaperones protect other proteins against misfolding and aggregation, a key requirement for maintaining biological function. Experimental observations of changes in solubility of amyloid proteins in the presence of certain chaperones are discussed here in terms of thermodynamic driving forces. We outline how chaperones can enhance amyloid solubility through the formation of heteromolecular aggregates (co-aggregates) based on the second law of thermodynamics and the flux towards equal chemical potential of each compound in all phases of the system. Higher effective solubility of an amyloid peptide in the presence of chaperone implies that the chemical potential of the peptide is higher in the aggregates formed under these conditions compared to peptide-only aggregates. This must be compensated by a larger reduction in chemical potential of the chaperone in the presence of peptide compared to chaperone alone. The driving force thus relies on the chaperone being very unhappy on its own (high chemical potential), thus gaining more free energy than the amyloid peptide loses upon forming the co-aggregate. The formation of heteromolecular aggregates also involves the kinetic suppression of the formation of homomolecular aggregates. The unhappiness of the chaperone can explain the ability of chaperones to favour an increased population of monomeric client protein even in the absence of external energy input, and with broad client specificity. This perspective opens for a new direction of chaperone research and outlines a set of outstanding questions that aim to provide additional cues for therapeutic development in this area.
Automatic discovery of photoisomerization mechanisms with nanosecond machine learning photodynamics simulations (2021)

Photochemical reactions are widely used by academic and industrial researchers to construct complex molecular architectures <i>via</i> mechanisms that often require harsh reaction conditions. Photodynamics simulations provide time-resolved snapshots of molecular excited-state structures required to understand and predict reactivities and chemoselectivities. Molecular excited-states are often nearly degenerate and require computationally intensive multiconfigurational quantum mechanical methods, especially at conical intersections. Non-adiabatic molecular dynamics require thousands of these computations per trajectory, which limits simulations to ∼1 picosecond for most organic photochemical reactions. Westermayr <i>et al.</i> recently introduced a neural-network-based method to accelerate the predictions of electronic properties and pushed the simulation limit to 1 ns for the model system, methylenimmonium cation (CH<sub>2</sub>NH<sub>2</sub> <sup>+</sup>). We have adapted this methodology to develop the Python-based, Python Rapid Artificial Intelligence <i>Ab Initio</i> Molecular Dynamics (PyRAI<sup>2</sup>MD) software for the <i>cis</i>-<i>trans</i> isomerization of <i>trans</i>-hexafluoro-2-butene and the 4π-electrocyclic ring-closing of a norbornyl hexacyclodiene. We performed a 10 ns simulation for <i>trans</i>-hexafluoro-2-butene in just 2 days. The same simulation would take approximately 58 years with traditional multiconfigurational photodynamics simulations. We generated training data by combining Wigner sampling, geometrical interpolations, and short-time quantum chemical trajectories to adaptively sample sparse data regions along reaction coordinates. The final data set of the <i>cis</i>-<i>trans</i> isomerization and the 4π-electrocyclic ring-closing model has 6207 and 6267 data points, respectively. The training errors in energy using feedforward neural networks achieved chemical accuracy (0.023-0.032 eV). The neural network photodynamics simulations of <i>trans</i>-hexafluoro-2-butene agree with the quantum chemical calculations showing the formation of the <i>cis</i>-product and reactive carbene intermediate. The neural network trajectories of the norbornyl cyclohexadiene corroborate the low-yielding <i>syn</i>-product, which was absent in the quantum chemical trajectories, and revealed subsequent thermal reactions in 1 ns.
Vibration insensitive interferometric optical testing (2004)

The measurement accuracy of an interferometric optical test is generally limited by the environment. This paper discusses two single-shot interferometric techniques for reducing the sensitivity of an optical test to vibration; simultaneous phase-shifting interferometry and spatial carrier interferometry.
Spectral-domain OCT changes in retina and optic nerve in children with hypoxic–ischaemic encephalopathy (2020)

Thickness reduction of inner retinal layer and peripapillary nerve fibre impairment was related to encephalopathy severity. Ocular damage was associated with inflammation and cerebral oedema following hypoxic-ischaemic damage.
An Agrobacterium VirE2 channel for transferred-DNA transport into plant cells (2001)

Transferred DNA (T-DNA) transfer from Agrobacterium tumefaciens into eukaryotic cells is the only known example of interkingdom DNA transfer. T-DNA is a single-stranded segment of Agrobacterium's tumor-inducing plasmid that enters the plant cell as a complex with the bacterial virulence proteins VirD2 and VirE2. The VirE2 protein is highly induced on contact of A. tumefaciens with a plant host and has been reported to act in late steps of transfer. One of its previously demonstrated functions is binding to the single-stranded (ss) T-DNA and protecting it from degradation. Recent experiments suggest other functions of the protein. A combination of planar lipid bilayer experiments, vesicle swelling assays, and DNA transport experiments demonstrated that VirE2 can insert itself into artificial membranes and form channels. These channels are voltage gated, anion selective, and single-stranded DNA-specific and can facilitate the efficient transport of single-stranded DNA through membranes. These experiments demonstrate a VirE2 function as a transmembrane DNA transporter, which could have applications in gene delivery systems.
Intranasal antigen targeting to MHC class II molecules primes local IgA and serum IgG antibody responses in mice (1997)

Covalent conjugates of hen egg lysozyme (HEL) and anti-major histocompatibility complex (MHC) class II monoclonal antibodies (mAb) were used to immunize mice intranasally. Three weeks after intranasal (IN) priming, mice responded rapidly to IN challenge with a mixture of HEL and cholera toxin (CT), by producing large titres of anti-HEL IgA and IgG1 antibody in serum, and IgA antibody in nasal secretions. No secondary response to HEL plus CT occurred in mice that received no priming or mice primed with HEL alone. The secondary serum IgG antibody response was dominated by the IgG1 subclass. HEL combined with CT adjuvant worked much better than HEL alone in producing the secondary response. Control conjugates, containing an IgG isotype-matched mAb without specificity for mouse tissues, provided poor priming. Mice expressing MHC class II molecules, to which the anti-MHC II mAb could not bind, produced a weak antibody response compared with those that expressed the appropriate. MHC class II molecule. Our results demonstrate that immunotargeting to MHC class II molecules via the IN route allows priming of the local IgA and circulating IgG antibody, and indicate that this technique is a feasible approach for delivery of subunit vaccines in the upper respiratory tract.
Passwords in the Air (2018)

Smart devices without an interactive UI (e.g., a smart bulb) typically rely on specific provisioning schemes to connect to wireless networks. Among all the provisioning schemes, SmartCfg is a popular technology to configure the connection between smart devices and wireless routers. Although the SmartCfg technology facilitates the Wi-Fi configuration, existing solutions seldom take into serious consideration the protection of credentials and therefore introduce security threats against Wi-Fi credentials.
A half-micron ferroelectric memory cell technology with stacked capacitor structure (2002)

A half-micron ferroelectric technology applicable to mega-bit non-volatile memories is reported. 10.5 /spl mu/m/sup 2/ 1transistor/1capacitor cell with a stacked capacitor structure is successfully achieved using planarization by CMP (chemical mechanical polishing), dry etching at the high temperature and TiO/sub 2/ diffusion barrier technologies. The capacitance above 50 fF is obtained at the size of 1.5 /spl mu/m/spl times/1.5 /spl mu/m, which satisfies the primary requirements for 4M NVDRAM operation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Geologic framework for the national assessment of carbon dioxide storage resources: Bighorn Basin, Wyoming and Montana: Chapter A in <i>Geologic framework for the national assessment of carbon dioxide storage resources</i> (2012)

The 2007
Deterioration of Oxygenation and Abnormal Lung Microvascular Permeability during Resolution of Leukopenia in Patients with Diffuse Lung Injury (1985)

To determine whether circulating leukocytes contribute to gas exchange abnormalities in diffuse lung injury, we retrospectively examined oxygenation in 6 patients who met 3 criteria: leukopenia caused by marrow aplasia from remission-inducing chemotherapy for myelogenous leukemia, the eventual resolution of leukopenia, and concurrent acute respiratory failure diagnosed clinically as increased permeability pulmonary edema. Four of the 6 patients abruptly developed overt clinical evidence of pulmonary dysfunction within the 96 h preceding the resolution of the peripheral leukopenia. In all 6 patients, the alveolar to arterial oxygen tension difference increased between leukocyte counts. The mean value for the alveolar to arterial oxygen tension difference for the group doubled during this period (148 +/- 37 mmHg 3 days prior to resolution; 290 +/- 37 mmHg 1 day after resolution; p less than 0.05). As an index of lung capillary permeability, we measured the lung permeability-surface area product for urea (PSu) for an additional patient with oxygen toxicity and drug-induced leukopenia whose hypoxemia increased immediately before the resolution of leukopenia. The PSu in this patient was high, in the range previously reported as being highly specific for increased permeability pulmonary edema with a fatal outcome. We conclude that such diffuse lung injury resembling the adult respiratory distress syndrome can occur in leukopenic patients, but the resolution of leukopenia in such patients may be associated with worsening oxygenation and with abnormally high pulmonary microvascular permeability. These observations do not prove a causal relationship but provide a clinical parallel to several leukocyte-depletion studies reported in animal models of increased permeability pulmonary edema that implicate white blood cells in the pathogenesis of hypoxemia and lung edema.
Optimal Design of the IRSBot-2 Based on an Optimized Test Trajectory (2013)

This paper deals with the design optimization of the IRSBot-2 based on an optimized test trajectory for fast pick and place operations. The IRSBot-2 is a two degree-of-freedom translational parallel manipulator dedicated to fast and accurate pick-and-place operations. First, an optimization problem is formulated to determine the optimal test trajectory. This problem aims at finding the path defined with s-curves and the time trajectory that minimize the cycle time while the maximum acceleration of the moving platform remains lower than 20 G and the time trajectory functions are C2 continuous. Then, two design optimization problems are formulated to find the optimal design parameters of the IRSBot-2 based on the previous optimal test trajectory. These two problems are formulated so that they can be solved in cascade. The first problem aims to define the design parameters that affect the geometric and kinematic performances of the manipulator. The second problem is about the determination of the remaining parameters by considering elastostatic and dynamic performances. Finally, the optimal design parameters are given and will be used for the realization of an industrial prototype of the IRSBot-2.
Amyloid β protein toxicity mediated by the formation of amyloid‐β protein precursor complexes (2003)

The amyloid-beta protein precursor, a type 1 transmembrane protein, gives rise to the amyloid beta-protein, a neurotoxic peptide postulated to be involved in the pathogenesis of Alzheimer's disease. Here, we show that soluble amyloid beta protein accelerates amyloid precursor protein complex formation, a process that contributes to neuronal cell death. The mechanism of cell death involves the recruitment of caspase-8 to the complex, followed by intracytoplasmic caspase cleavage of amyloid precursor protein. In vivo, the levels of soluble amyloid beta protein correlated with caspase-cleaved fragments of the amyloid precursor protein in brains of Alzheimer's disease subjects. These findings suggest that soluble amyloid beta protein-induced multimerization of the amyloid precursor protein may be another mechanism by which amyloid beta protein contributes to synapse loss and neuronal cell death seen in Alzheimer's disease.
Data from Bortezomib induces apoptosis in esophageal squamous cell carcinoma cells through activation of the p38 mitogen-activated protein kinase pathway (2023)

&lt;div&gt;Abstract&lt;p&gt;Esophageal squamous cell carcinoma (ESCC) is an exceptionally drug-resistant tumor with a 5-year survival rate &lt;5%. From an initial drug screen, we identified bortezomib as having robust activity in ESCC lines. Mechanistically, bortezomib induced a G&lt;sub&gt;2&lt;/sub&gt;-M-phase cell cycle arrest and p53-independent apoptosis associated with caspase cleavage and Noxa induction. Bortezomib also showed excellent activity in organotypic culture and &lt;i&gt;in vivo&lt;/i&gt; models of ESCC. Biochemically, bortezomib treatment activated the p38 and c-Jun NH&lt;sub&gt;2&lt;/sub&gt;-termnial kinase stress-activated mitogen-activated protein kinase (MAPK) pathways and induced phospho-H2AX activity. Although H2AX is known to cooperate with c-Jun NH&lt;sub&gt;2&lt;/sub&gt;-termnial kinase to induce apoptosis following UV irradiation, knockdown of H2AX did not abrogate bortezomib-induced apoptosis. Instead, blockade of p38 MAPK signaling, using either small interfering RNA or a pharmacologic inhibitor, reversed bortezomib-induced apoptosis and the up-regulation of Noxa. Radiation therapy is known to activate the p38 MAPK pathway and is a mainstay of ESCC treatment strategies. In a final series of studies, we showed that the coadministration of bortezomib with irradiation led to enhanced p38 MAPK activity and a significant reduction in colony formation. We therefore suggest that p38 MAPK pathway activation is an excellent potential therapeutic strategy in ESCC. It is further suggested that bortezomib could be added to existing ESCC therapeutic regimens. [Mol Cancer Ther 2008;7(9):2866–75]&lt;/p&gt;&lt;/div&gt;
Switch from a type 2 to a type 1 T helper cell response and cure of established Leishmania major infection in mice is induced by combined therapy with interleukin 12 and Pentostam. (1995)

Successful treatment in allergic, autoimmune, and infectious diseases often requires altering the nature of a detrimental immune response mediated by a particular CD4+ T helper (Th) cell subset. While several factors contribute to the development of CD4+ Th1 and Th2 cells, the requirements for switching an established response are not understood. Here we use infection with Leishmania major as a model to investigate those requirements. We report that treatment with interleukin 12 (IL-12), in combination with the antimony-based leishmanicidal drug Pentostam, induces healing in L. major-infected mice and that healing is associated with a switch from a Th2 to a Th1 response. The data suggest that decreasing antigen levels may be required for IL-12 to inhibit a Th2 response and enhance a Th1 response. These observations are important for treatment of nonhealing forms of human leishmaniasis and also demonstrate that in a chronic infectious disease an inappropriate Th2 response can be switched to an effective Th1 response.
Optical Analysis of Ball Bearing Starvation (1971)

Elastohydrodynamic oil film measurements for rolling point contact under starvation conditions are obtained using optical interferometry. The experimental measurements present a reasonably clear picture of the starvation phenomenon and are shown to agree with theoretical predictions. Starvation inhibits the generation of pressure and, therefore, reduces film thickness. It also causes the overall pressure, stress, and elastic deformation to become more Hertzian. Additional experiments using interferometry illustrate: the cavitation pattern, lubricant entrapment, grease lubrication, ball spin, and edge effects in line contact.
An Affordable Custom-Built Negative Pressure Wound Therapy (2017)

Negative pressure wound therapy (NPWT) is a wellestablished and effective method for treating complex wounds. However, this modality of treatment may not be available in limited resource countries due to the high cost. We describe a simple and cheap method of NPWT using gauze swabs, a naso-gastric tube, adhesive occlusive drape and a central or portable suction machine.Key words: Negative Pressure, Wound Therapy