gebhart/patrepeval huggingface dataset:
Equitable Sequencing of a Given Set of Hazardous Materials Shipments (1991)

In a recent paper, R. Gopalan, K. Kolluri, R. Batta and M. Karwan (1990) consider a model to route a set of hazardous materials shipments from an origin to a destination, so as to minimize the global risk to the community while simultaneously maintaining a desired level of equity between zones within the community. If one follows the routes produced via their solution methodology, the overall risk is small and equity between zones is achieved after all the shipments are over. However, equity may be severely violated at an intermediate stage of the shipment process. Since an accident can occur at any stage, this is not a desirable situation. Motivated by this, in this paper we consider the problem of equitably sequencing a given set of hazardous materials shipments. We presume, of course, that the set of routes are such that they engender low overall risk to the community as a whole, and once they are all traversed the risk is equitably distributed among the zones of the community—Gopalan, Kolluri, Batta, and Karwan's paper provides such routes for the case of a single origin and destination; their procedure is easily adaptable for the case of multiple origins and destinations. The objective function considered in this paper is to minimize the sum of the maximum differences in risk that exist between any two zones, where the sum is taken over the trips made. We formulate the resulting equitable sequencing problem as an integer programming problem and as a dynamic programming problem. Optimal solution strategies are examined for small-sized problems. Several heuristic solution strategies are proposed to obtain the upper bounds needed for dynamic programming fathoming and for obtaining reasonable solutions to large-sized problems. The proposed solution methods are tested on a real data set from the City and County of Albany, New York, as well as on a randomly generated data set.
Affinity Chromatography with Specific Antibody Increases Activity and Retains Antigenicity of Ornithine Decarboxylase (1982)

An affinity chromatography column with antibody specific to ornithine decarboxylase (ODC) was employed successfully for the retention and subsequent partial elution of ODC with enhanced activity and retention of antigenicity. This may be a useful procedure for further attempts to produce antiserum for identification and characterizations of ODC in vitro and in vivo.
Circulation of Dengue Virus Serotype 2 in Humans and Mosquitoes During an Outbreak in El Quseir City, Egypt (2022)

This was the first serotyping of the DENV responsible for dengue virus outbreak in Egypt in 2017. Determining the serotype of dengue virus can help to avoid and monitor outbreaks. The serotype identified in this study was DENV-2, while DENV-1 was the serotype found in the previous outbreak in 2015 in the province of Assiut. This study thus raises concerns that a new dengue serotype could have been introduced into Egypt. It is necessary for a comprehensive risk assessment to be carried out in the country, including an entomological survey, to assess the presence and potential geographical expansion of mosquito vectors there.
Epitranscriptomics in Hematopoiesis and Hematologic Malignancies (2020)

Since the 1960s, a large number of chemical modifications have been identified in RNA molecules, establishing the RNA epigenetics field named "epitranscriptomics." These chemical marks participate in several RNA metabolic processes; however, the biological relevance of many of these modifications and the many enzymes involved in their function is not completely understood. Emerging knowledge of the epitranscriptome (pseudouridine, N<sup>6</sup>-methyladenosine, and A-to-I editing) in hematopoiesis and hematologic malignancies reveals the requirement of these modifications in normal development and their alteration in disorders, leading to the development of new molecules and strategies to target the epitranscriptome as a novel therapeutic approach. RNA modifications are required for the correct development of hematopoietic cells, and their alteration can promote the development of malignancies or the transition from a low-grade to an aggressive disease. While we are expanding our understanding of the epitranscriptome of normal and malignant hematopoiesis, the number of potential new therapeutic interventions is rising.
Employing multiplex immunofluorescence to quantify Her2 and phosphorylated Her2 in formalin-fixed, paraffin-embedded breast tumor specimens (2009)

There has been progress in the identification of factors that confer important risk for the development of breast cancer. The factors include: heritable mutations in susceptibility genes; exposure to therapeutic radiation during breast development (as for Hodgkin's disease survivors who received therapeutic radiation to the chest); and histologic lesions, including LCIS and atypical hyperplasias. Testing for mutations in the BRCA1 and BRCA2 breast ovarian cancer susceptibility genes has become part of the established care of breast cancer patients. Genetic information from BRCA1/2 testing is used to help healthy at-risk women to avoid breast and/or ovarian cancer, and ultimately to avoid death from those cancers. Data accumulated over the past decade have provided evidence that breast cancer surveillance can be improved with the addition of breast MRI, that prophylactic oophorectomy substantially reduces the risk of ovarian cancer and, when performed before menopause, can reduce the risk of breast cancer as well, and that prophylactic mastectomy reduces the risk of breast cancer by more than 90%. It has been observed that approximately 80% of BRCA1-associated breast cancers are negative for ER, PR and HER2 (so-called triple negative) and cluster with basal-like breast cancers by DNA microarray, while 80% of BRCA2-associated breast cancers are ER + and PR + , but HER2 negative, and luminal. These data are surprising given the close relationships between these genes in their DNA repair activities, and raise some concern that hormonal interventions will not successfully reduce the risk of BRCA1-associated breast cancers. Other strategies may be necessary to reduce breast cancer risk for this group. Genetic information has been shown to have important implications for women with breast cancer as well. Women with strong family histories of breast and/or ovarian cancer, and women diagnosed before age 40 may consider testing at the time of breast cancer diagnosis if they would use the information to make treatment decisions. Some women choose bilateral mastectomies over breast-conserving treatment if they learn that their risk of second primary breast cancer exceeds 50%, and if their prognosis from the original breast cancer is good. Some women opt for oophorectomy as part of the management of their ER + breast cancer if they are premenopausal mutation carriers (and could participate in TEXT).
Data from Validation of the Hsp70–Bag3 Protein–Protein Interaction as a Potential Therapeutic Target in Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Hsp70 is a stress-inducible molecular chaperone that is required for cancer development at several steps. Targeting the active site of Hsp70 has proven relatively challenging, driving interest in alternative approaches. Hsp70 collaborates with the Bcl2-associated athanogene 3 (Bag3) to promote cell survival through multiple pathways, including FoxM1. Therefore, inhibitors of the Hsp70–Bag3 protein–protein interaction (PPI) may provide a noncanonical way to target this chaperone. We report that JG-98, an allosteric inhibitor of this PPI, indeed has antiproliferative activity (EC&lt;sub&gt;50&lt;/sub&gt; values between 0.3 and 4 μmol/L) across cancer cell lines from multiple origins. JG-98 destabilized FoxM1 and relieved suppression of downstream effectors, including p21 and p27. On the basis of these findings, JG-98 was evaluated in mice for pharmacokinetics, tolerability, and activity in two xenograft models. The results suggested that the Hsp70–Bag3 interaction may be a promising, new target for anticancer therapy. &lt;i&gt;Mol Cancer Ther; 14(3); 642–8. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Deletion of Men1 and somatostatin induces hypergastrinemia and gastric carcinoids (2016)

Gastric carcinoids require threshold levels of hypergastrinemia, which modulates p27<sup>Kip1</sup> cellular location and stability.
Ultra-compact low-loss broadband waveguide taper in silicon-on-insulator (2017)

A novel design of large bandwidth, fabrication tolerant, CMOS-compatible compact tapers (15 um) have been proposed and experimentally demonstrated in silicon-on-insulator. The proposed taper along with linear grating couplers for spot-size conversion exhibits no degradation in the coupling efficiency compared to a standard focusing grating in 1550 nm band. A single taper design has a broadband operation over 600 nm that can be used in O, C and L-band. The proposed compact taper is highly tolerant to fabrication variations; 80 nm change in the taper width and 200 nm in end waveguide width varies the taper transmission by <0.4 dB. The footprint of the device i.e. taper along with the linear gratings is ~ 250 {\mu}m2; this is 20X smaller than the adiabatic taper and 2X smaller than the focusing grating coupler.
Expert Gate: Lifelong Learning with a Network of Experts (2016)

In this paper we introduce a model of lifelong learning, based on a Network of Experts. New tasks / experts are learned and added to the model sequentially, building on what was learned before. To ensure scalability of this process,data from previous tasks cannot be stored and hence is not available when learning a new task. A critical issue in such context, not addressed in the literature so far, relates to the decision which expert to deploy at test time. We introduce a set of gating autoencoders that learn a representation for the task at hand, and, at test time, automatically forward the test sample to the relevant expert. This also brings memory efficiency as only one expert network has to be loaded into memory at any given time. Further, the autoencoders inherently capture the relatedness of one task to another, based on which the most relevant prior model to be used for training a new expert, with finetuning or learning without-forgetting, can be selected. We evaluate our method on image classification and video prediction problems.
Accelerated Stack-of-Spirals Free-Breathing Three-Dimensional Ultrashort Echo Time Lung Magnetic Resonance Imaging: A Feasibility Study in Patients With Breast Cancer (2021)

Accelerated free-breathing spiral 3D UTE using the SPIRiT algorithm could be a potential alternative to CT for oncology patients.
Alternative Radwaste Solidification Route for Three Mile Island Wastes (1982)

Present plans being considered for Three Mile Island (TMI) wastes involve radionuclide adsorption on zeolites, transportation, and possible melting with pit into glass. Several zeolites were treated with a simulated TMI waste and directly sintered at 1000°C to fix the adsorbed ions. The Cs leach rates of the sintered products are similar to those of borosilicate glasses. Thus, simple sintering (on‐site) of zeolites may be a cost‐effective and less cumbersome alternative for such waste solidification.
Perforin gene expression in granular lymphocyte proliferative disorders (1990)

By Northern blot analysis using a cDNA clone of the perforin gene, we studied the levels of perforin mRNA in peripheral blood mononuclear cells from 11 cases of granular lymphocyte-proliferative disorders (GLPDs). The granular lymphocytes studied were characterized by morphologic, immunophenotypic, and immunogenotypic analyses. Cytolytic functions of the lymphocytes assayed included nonmajor histocompatibility complex-requiring cytotoxicity, anti-CD3-redirected cytotoxicity, antibody-dependent cellular cytotoxicity, and lectin- dependent cellular cytotoxicity. The results showed that in lymphocytes with strong cytolytic functions high levels of perforin mRNA existed, whereas in lymphocytes with weak or undetectable levels of cytolytic functions, low levels of perforin mRNA existed. Because the levels of perforin mRNA correlated with those of cytolytic functions, perforin is probably a mediator in cytolytic functions of granular lymphocytes in patients with GLPDs. When the lymphocytes were cultured for 1 day, however, the levels of cytolytic activity were increased, and those of perforin mRNA were decreased. Therefore, we cannot rule out the possibility that factors other than perforin protein are involved in the cytolytic functions of granular lymphocytes.
[18F]ODIBO: a prosthetic group for bioorthogonal radiolabeling of macromolecules via strain-promoted alkyne–azide cycloaddition (2017)

A novel prosthetic group for the efficient radiolabeling of macromolecules has been developed. [<sup>18</sup>F]oxadibenzocyclooctyne ([<sup>18</sup>F]ODIBO) is synthesized in high radiochemical yield and applied for nearly quantitative conjugation to azide-tagged peptides and proteins at room temperature and low substrate concentrations. The resulting bioconjugates are chemically and radiochemically pure and free of toxic solvents and catalysts.
Oxidation Apparatus for Determining Rates of Oxygen Absorption of Lubricants (1971)

An oxidation apparatus is described which continuously records the volume of oxygen absorbed by a sample of oil, in a closed system, maintained at constant temperature and pressure. The apparatus is automated through the use of a specially devised liquid level probe and other ancillary equipment such as recorders, timers, and temperature controllers. The apparatus can be used to compare the relative oxidation stability of various lubricants over a wide range of operating conditions.
LSD-StructureNet: Modeling Levels of Structural Detail in 3D Part\n Hierarchies (2021)

Generative models for 3D shapes represented by hierarchies of parts can\ngenerate realistic and diverse sets of outputs. However, existing models suffer\nfrom the key practical limitation of modelling shapes holistically and thus\ncannot perform conditional sampling, i.e. they are not able to generate\nvariants on individual parts of generated shapes without modifying the rest of\nthe shape. This is limiting for applications such as 3D CAD design that involve\nadjusting created shapes at multiple levels of detail. To address this, we\nintroduce LSD-StructureNet, an augmentation to the StructureNet architecture\nthat enables re-generation of parts situated at arbitrary positions in the\nhierarchies of its outputs. We achieve this by learning individual,\nprobabilistic conditional decoders for each hierarchy depth. We evaluate\nLSD-StructureNet on the PartNet dataset, the largest dataset of 3D shapes\nrepresented by hierarchies of parts. Our results show that contrarily to\nexisting methods, LSD-StructureNet can perform conditional sampling without\nimpacting inference speed or the realism and diversity of its outputs.\n
Esthesioneuroblastoma: An Update on the Ucla Experience 2002-2013 (2014)

Introduction: Esthesioneuroblastomas are rare malignant tumors of the superior nasal vault. Controversy exists surrounding optimal treatments and staging systems that best predict survival. Here, we report an update on the UCLA experience and identify prognostic factors for survival and also provide an update on the surgical techniques being utilized.
Treating Diabetic Foot Osteomyelitis Primarily With Surgery or Antibiotics: Have We Answered the Question? (2014)

Foot infections are among the most frequent diabetes-related causes for hospitalization and the usual immediate predecessor to lower-extremity amputation in these patients (1). Infection usually starts in ulcerated soft tissues, but can spread contiguously to underlying bone (2). Overall, about 20% of patients with a diabetic foot infection (and over 60% of those with severe infections [3]) have underlying osteomyelitis, which dramatically increases the risk of lower-extremity amputation (4). Indeed, optimally managing diabetic foot osteomyelitis is widely considered the most difficult and controversial aspect of dealing with diabetic foot infections (5–7).

In the preantibiotic era, the only option for treating osteomyelitis was surgical resection of all necrotic and infected bone. Because surgeons feared further spread of infection up the limb in what was then called “diabetic gangrene,” most procedures were major (often above the knee) amputations (8). The advent of antibiotic therapy led to a marked reduction in both mortality (9–11) and need for major amputations (10,11) in patients with diabetic foot infections. Antibiotic therapy was largely considered adjunctive to surgery, but in the past two decades reports appeared of patients with diabetic foot osteomyelitis apparently cured by antibiotic therapy with little or no surgical resection (12), leading some to reexamine the belief that surgery was almost always needed for this form of chronic osteomyelitis (13).

There are potential advantages, as well as disadvantages, to both medical and surgical treatment of diabetic foot osteomyelitis (Table 1). In some clinical situations, it is clear that one or the other approach is most appropriate (Table 2), but in most cases the …
Halogen-bonded liquid-crystalline complexes formed from 4-alkoxyphenylpyridines with iodine and with interhalogens (2023)

Strongly halogen-bonded complexes form between 4-alkoxyphenyl-4-pyridines and iodine as well as the interhalogens ICl and IBr. Examples are characterised by single crystal X-ray crystallography and most complexes show a liquid-crystalline SmA phase.
Neonatal exposure to staphylococcal superantigen improves induction of oral tolerance in a mouse model of airway allergy (2009)

The hygiene hypothesis suggests that lack of microbial stimulation in early infancy may lead to allergy, but it has been difficult to identify particular protective microbial exposures. We have observed that infants colonised in the first week(s) of life with Staphylococcus aureus have lower risk of developing food allergy. As many S. aureus strains produce superantigens with T-cell stimulating properties, we here investigate whether neonatal mucosal exposure to superantigen could influence the capacity to develop oral tolerance and reduce sensitisation and allergy. BALB/c mice were exposed to staphylococcal enterotoxin A (SEA) as neonates and fed with OVA as adults, prior to sensitisation and i.n. OVA challenge. Our results show that SEA pre-treated mice are more efficiently tolerised by OVA feeding, as shown by lower lung-cell infiltration and antigen-specific IgE response in the SEA pre-treated mice, compared with sham-treated mice. This was not due to deletion or anergy of lymphocytes by SEA treatment, because the SEA pre-treated mice that were fed with PBS showed similar inflammatory response as the sham-treated PBS-fed mice. Our results suggest that strong T-cell activation in infancy conditions the mucosal immune system and promotes development of oral tolerance.
Mutant Huntingtin Affects Cortical Progenitor Cell Division and Development of the Mouse Neocortex (2014)

A polyglutamine expansion in huntingtin (HTT) causes the specific death of adult neurons in Huntington's disease (HD). Most studies have thus focused on mutant HTT (mHTT) toxicity in adulthood, and its developmental effects have been largely overlooked. We found that mHTT caused mitotic spindle misorientation in cultured cells by altering the localization of dynein, NuMA, and the p150(Glued) subunit of dynactin to the spindle pole and cell cortex and of CLIP170 and p150(Glued) to microtubule plus-ends. mHTT also affected spindle orientation in dividing mouse cortical progenitors, altering the thickness of the developing cortex. The serine/threonine kinase Akt, which regulates HTT function, rescued the spindle misorientation caused by the mHTT, by serine 421 (S421) phosphorylation, in cultured cells and in mice. Thus, cortical development is affected in HD, and this early defect can be rescued by HTT phosphorylation at S421.
Surgical Risks and Costs of Care are Greater in Patients Who Are Super Obese and Undergoing THA (2016)

Level III, therapeutic study.
Constitutive models for a poly(e-caprolactone) scaffold. (2004)

We investigate material models for a porous, polymeric scaffold used for bone. The material was made by co-extruding poly(e-caprolactone) (PCL), a biodegradable polyester, and poly(ethylene oxide) (PEO). The water soluble PEO was removed resulting in a porous scaffold. The stress-strain curve in compression was fit with a phenomenological model in hyperbolic form. This material model will be useful for designers for quasi-static analysis as it provides a simple form that can easily be used in finite element models. The ASTM D-1621 standard recommends using a secant modulus based on 10% strain. The resulting modulus has a smaller scatter in its value compared to the coefficients of the hyperbolic model, and it is therefore easier to compare material processing differences and ensure quality of the scaffold. A third material model was constructed from images of the microstructure. Each pixel of the micrographs was represented with a brick finite element and assigned the Young's modulus of bulk PCL or a value of 0 for a pore. A compressive strain was imposed on the model and the resulting stresses were calculated. The elastic constants of the scaffold were then computed using Hooke's law for a linear-elastic isotropic material. The model was able to predict the small strain Young's modulus measured in the experiments to within one standard deviation. Thus, by knowing the microstructure of the scaffold, its bulk properties can be predicted from the material properties of the constituents.
Methylation and tautomerism of 5-fluorocytosine nucleosides and their analogues (1978)

ABSTRACTt The aminatian of 1,3-dimethyl-5-fluaro-4-thiouracil in ethanolic medium at elevated temperatures has been investigated. The N--methyl, fixed imino, analogues of 5-fluorocytidine, 1-0-D-arabinofuranosyl-5-fluorocytosine and 1-iethyl-5-fluorocytosine were prepared by diazcmethane treatment, and some of their properties are described. In particular the basicity method was applied to determine the imino/amino tautomeric equilibrium constants ( i c ) for the 5-halogenocytosine nudeosides relative to cytidine, and the possible relevance of these results to mutagenesis by 5-halogenopyrimidine nudeosides.
Study of neutron damage in GaAs MESFETs (1997)

Implanted channel GaAs MESFETs subjected to neutron irradiation show large modifications of the pinch-off voltage, open-channel saturation current, and transconductance in agreement with previous results. In this work we demonstrate how an experimental technique, based on the frequency dispersion of the transconductance, g/sub m/(f), and output conductance, g/sub D/(f), can identify the deep levels induced by neutron irradiation through measurements performed directly on packaged devices. After irradiation, a frequency dispersion of the transconductance has been observed, while it was flat in the unirradiated device. The g/sub m/(f) curve shape depends on the device bias conditions, and it has permitted for the first time to evaluate the activation energy of different deep levels induced by neutron irradiation in MESFETs.