gebhart/patrepeval huggingface dataset:
Maternal dietary choline availability alters the balance of netrin-1 and DCC neuronal migration proteins in fetal mouse brain hippocampus (2005)

Alterations in maternal dietary choline availability during days 12-17 of pregnancy led to an increase in the level of immunoreactive netrin-1 and a decrease in the level of DCC protein in the developing fetal mouse brain hippocampus compared with controls. Changes in the expression of cell migration cues during development could account for some of the lifelong consequences of maternal dietary choline availability for cognitive and memory processes.
CDK-dependent complex formation between replication proteins Dpb11, Sld2, Pol ɛ, and GINS in budding yeast (2010)

Eukaryotic chromosomal DNA replication requires cyclin-dependent kinase (CDK) activity. CDK phosphorylates two yeast replication proteins, Sld3 and Sld2, both of which bind to Dpb11 when phosphorylated. These phosphorylation-dependent interactions are essential and are the minimal requirements for CDK-dependent activation of DNA replication. However, how these interactions activate DNA replication has not been elucidated. Here, we show that CDK promotes the formation of a newly identified fragile complex, the preloading complex (pre-LC) containing DNA polymerase epsilon (Pol epsilon), GINS, Sld2, and Dpb11. Formation of the pre-LC requires phosphorylation of Sld2 by CDK, but is independent of DNA replication, protein association with replication origins, and Dbf4-dependent Cdc7 kinase, which is also essential for the activation of DNA replication. We also demonstrate that Pol epsilon, GINS, Dpb11, and CDK-phosphorylated Sld2 form a complex in vitro. The genetic interactions between Pol epsilon, GINS, Sld2, and Dpb11 suggest further that they form an essential complex in cells. We propose that CDK regulates the initiation of DNA replication in budding yeast through formation of the pre-LC.
Framework of Big Data and Deep Learning for Simultaneously Solving Space Allocation and Signal Timing Problem (2022)

Efficient operations at intersections are associated with smooth, safe, and sustainable travel at the network level. It is often challenging to prevent congestion at these locations, especially during rush hours, owing to high traffic demand and restraints of road geometry. The primary cause of intersection traffic congestion is large variations and fluctuations in traffic demand during the day. Dynamic lane assignment (DLA) is an intelligent transportation system (ITS) technology that can improve traffic operations at signalized intersections, making better use of available space by optimizing lane allocation based on real-time fluctuating traffic demands. This study used a brute-force optimization model to produce a vast synthetic dataset of turning movements at a four-legged signalized intersection. The model then found the optimal lane assignment and cycle length for each case. The produced data were used to develop a deep learning model to predict the optimal lane assignment and cycle length simultaneously at any four-legged signalized intersection without applying optimization software per se. The deep learning model results developed were compared with the results of the k-nearest neighbors (KNN), random forest, and decision tree algorithms. It was found that the deep learning model was superior, with accuracy and F1 score of 95.26% and 93.56%, respectively. The proposed solution is expected to require insignificant additional resources and services for successful implementation, particularly in developing countries.
Limb lengthening by diaphyseal corticotomy, callus distraction, and dynamic axial fixation. An experimental study in the ovine femur (1988)

Limb lengthening of the left femur was performed in 12 sheep, 7-8 months of age. After weakening of the cortex by drill holes, a controlled fracture was created in the diaphysis. The bone segments were fixed in reduced position using a unilateral external fixation device. The fixator was left in neutral position for 10 days postoperatively when lengthening started. By means of daily distraction at a rate of 1.0 mm once a day for 3 weeks, an average lengthening of 1.9 cm (11.9%) was obtained. Two weeks after distraction had been discontinued, distinct callus bridging of the lengthening zone was confirmed radiographically in all animals. At this time the rigid state of fixation was converted to a system allowing axial compression by loading in half the animals. The other half of the animals served as controls with the fixator remaining unchanged. The external device was left on until 5 weeks after the end of distraction. At this time the animals were killed. Both femora of all animals were tested mechanically in torsion. The average ultimate torsional strength of the elongated femur compared with control was 71% in the group with dynamic axial fixation and 65% in the control group. No significant difference in relative strength of the tested bones in the two groups was found. We conclude that intermittent axial compression by loading during consolidation had no significant effect on the bone-healing process evaluated by radiography and mechanical testing.
Supplementary Table 1 from BAFF Attenuates Immunosuppressive Monocytes in the Melanoma Tumor Microenvironment (2023)

&lt;p&gt;Supplementary Table 1 provides a list of significantly changed genes between monocytes harvested from BAFF and control tumors&lt;/p&gt;
Qualified Biolayer Interferometry Avidity Measurements Distinguish the Heterogeneity of Antibody Interactions with Plasmodium falciparum Circumsporozoite Protein Antigens (2018)

Ab avidity is a measure of the overall strength of Ab-Ag interactions and hence is important for understanding the functional efficiency of Abs. In vaccine evaluations, Ab avidity measurements can provide insights into immune correlates of protection and generate hypotheses regarding mechanisms of protection to improve vaccine design to achieve higher levels of efficacy. The commonly used Ab avidity assays require the use of chaotropic reagents to measure avidity index. In this study, using real-time detection of Ab-Ag binding by biolayer interferometry (BLI) technique, we have developed a qualified assay for measuring avidity of vaccine-induced Abs specific for <i>Plasmodium falciparum</i> circumsporozoite protein (CSP) Ags. Human mAb derived from plasmablasts of recipients of RTS,S/AS01 (RTS,S), the most advanced malaria vaccine candidate, were used in the assay development to measure Ag-specific binding responses and rate constants of association and dissociation. The optimized BLI binding assay demonstrated 1) good precision (percentage of coefficient of variation <20), 2) high specificity, 3) a lower limit of detection and quantitation in the 0.3-3.3 nM range, and 4) a range of linearity up to 50-100 nM for the CSP Ags tested. Analysis of polyclonal sera of malaria vaccinees demonstrated the suitability of this method to distinguish among vaccinees and rank Ab responses by avidity. These results demonstrate that precise, specific, and sensitive BLI measurements of Ab avidity in polyclonal sera from malaria vaccinees can map Ab response heterogeneity and potentially help to determine the role of Ab avidity as an immune correlate of protection for vaccines.
MIT Space Engineering Research Center (1990)

The Space Engineering Research Center (SERC) at MIT, started in Jul. 1988, has completed two years of research. The Center is approaching the operational phase of its first testbed, is midway through the construction of a second testbed, and is in the design phase of a third. We presently have seven participating faculty, four participating staff members, ten graduate students, and numerous undergraduates. This report reviews the testbed programs, individual graduate research, other SERC activities not funded by the Center, interaction with non-MIT organizations, and SERC milestones. Published papers made possible by SERC funding are included at the end of the report.
Leveraging Clinical Time-Series Data for Prediction: A Cautionary Tale (2018)

In healthcare, patient risk stratification models are often learned using time-series data extracted from electronic health records. When extracting data for a clinical prediction task, several formulations exist, depending on how one chooses the time of prediction and the prediction horizon. In this paper, we show how the formulation can greatly impact both model performance and clinical utility. Leveraging a publicly available ICU dataset, we consider two clinical prediction tasks: in-hospital mortality, and hypokalemia. Through these case studies, we demonstrate the necessity of evaluating models using an outcome-independent reference point, since choosing the time of prediction relative to the event can result in unrealistic performance. Further, an outcome-independent scheme outperforms an outcome-dependent scheme on both tasks (In-Hospital Mortality AUROC .882 vs. .831; Serum Potassium: AUROC .829 vs. .740) when evaluated on test sets that mimic real-world use.
Biochemical Methods and Assays (1994)

The tachykinins are a family of peptides that share the common C-terminal sequence These peptides exert their biological effects via three pharmacologically and molecular biologically well-defined receptors (see other chapters in this volume), the receptors. Substance P (SP) binds preferentially to the receptor, neurokinin A (NKA) to the receptor, and neurokinin B (NKB) to the receptor. Among other things, the number of receptor sites in tissues/cells and the affinities of compounds/peptides can be measured readily in receptor binding assays that exist for each individual tachykinin receptor. In this chapter, we will describe the development of these assays and the various factors that can influence their outcome. For reasons of clarity, the current tachykinin receptor nomenclature has been used throughout the chapter.
A low power and ultra high reliability LDPC error correction engine with Digital Signal Processing for embedded NAND Flash Controller in 40nm COMS (2014)

A multi-mode Low-Density Parity-Check (LDPC) error correction engine with a Digital Signal Processing (DSP) module is presented for low power and ultra high reliability NAND Flash memory controllers. The DSP module improves the reliability of the storage systems via calculating the adaptive reliability information and translating the information into Log-Likelihood Ratio (LLR) for soft bit decoding. According to the experiment results on sub-20nm Triple Level per Cell (TLC) NAND Flash memory, the retention ability of LDPC with DSP is a 20 times improvement over BCH code and 2 to 5 times improvement over conventional LDPC. Moreover, the proposed decoder reaches a throughput over 400MB/s as well as a power consumption of 21.8mW under 40nm CMOS technology at 45 bit errors.
Fabrication of Complex-Shape Products From a Binder-Free Green Composite Using Bamboo Fibers and Powders Extracted With a Machining Center (2017)

Research is currently ongoing for composite materials using natural fiber with a small burden on the environment. We have been focusing on bamboo because of its fast growth, renewability, flexibility, low cost, and high specific strength. We previously proposed a novel hot press fabrication method for binder-free green composite products made from bamboo fibers extracted by end-milling with a machining center. We can use this method to form three-dimensionally shaped products, especially hemispherical shells, by using two kinds of dies. However, this method is complex and takes longer than one-step hot press forming. In the present report, we propose a new method that uses bamboo powder with a particle size of less than 500 μm. Our new method uses one-step hot press forming and is quicker than the previous method at making a hemispherical shell shape. The new method was successfully used to manufacture hemispherical shell-shape products.
Recent Advances in Stabilization of Sodium Metal Anode in Contact with Organic Liquid and Solid‐State Electrolytes (2022)

Sodium (Na) metal is considered as the promising anode for next‐generation high‐energy‐density Na‐metal batteries owing to its highest specific capacity and lowest electrochemical potential among all Na‐based anode candidates. However, the Na metal anode suffers from considerable volume change, nonuniform Na deposition, and an unstable electrode–electrolyte interface, which result in rapid capacity fade and poor cycling stability, hampering its practical application. To tackle aforementioned issues, many strategies have been developed to accommodate and guide Na nucleation/growth as well as stabilize the interface, including structure stabilization by applying 3D host materials, electrolyte modification and interface engineering to form stable interfaces and guide the Na deposition, etc. The present review is intended as a guideline through the fundamental challenges affecting the performance of Na metal anodes along with corresponding mitigation strategies. Moreover, the specific mechanisms for stabilizing Na metal anodes are discussed in detail. Apart from the stabilization of the Na metal anode in contact with liquid electrolytes, attention has also been paid to the review of stabilization of the Na metal anode in contact with solid‐state electrolytes. Furthermore, unresolved challenges and promising perspectives for stable Na metal anodes in practical applications are presented.
Probabilistic Programming with Stochastic Probabilities (2023)

We present a new approach to the design and implementation of probabilistic programming languages (PPLs), based on the idea of stochastically estimating the probability density ratios necessary for probabilistic inference. By relaxing the usual PPL design constraint that these densities be computed exactly, we are able to eliminate many common restrictions in current PPLs, to deliver a language that, for the first time, simultaneously supports first-class constructs for marginalization and nested inference, unrestricted stochastic control flow, continuous and discrete sampling, and programmable inference with custom proposals. At the heart of our approach is a new technique for compiling these expressive probabilistic programs into randomized algorithms for unbiasedly estimating their densities and density reciprocals. We employ these stochastic probability estimators within modified Monte Carlo inference algorithms that are guaranteed to be sound despite their reliance on inexact estimates of density ratios. We establish the correctness of our compiler using logical relations over the semantics of λ SP , a new core calculus for modeling and inference with stochastic probabilities. We also implement our approach in an open-source extension to Gen, called GenSP, and evaluate it on six challenging inference problems adapted from the modeling and inference literature. We find that: (1) ‍can automate fast density estimators for programs with very expensive exact densities; (2) convergence of inference is mostly unaffected by the noise from these estimators; and (3) our sound-by-construction estimators are competitive with hand-coded density estimators, incurring only a small constant-factor overhead.
Visible emission from amorphous AlN thin-film phosphors with Cu, Mn, or Cr (2001)

Luminescence studies of amorphous AlN incorporated with pure Cu, Mn, or Cr and codeposited with (Cu, Tb, Mn) were performed at 300 K. Thin films of Cu, Mn, and Cr amorphous AlN, ∼200 nm thick, were grown on p-Si(111) substrates using rf magnetron sputtering in a nitrogen atmosphere. Cathodoluminescence showed that pure Cu incorporated amorphous AlN films have strong emission in the blue (∼420 nm) and Mn and Cr incorporated films luminescence in the red (∼690 nm). Cr3+ emission is likely more intense than Mn4+ because chromium does not suffer from incomplete charge compensation in the III–V semiconductor. Luminescence studies of layered structures where pure Cu incorporated films are grown on top of pure Cr incorporated films reveal emission from both Cr and Cu ions. The migration of Cr ions during the 1000 °C luminescence activation step is confirmed with secondary ion mass spectrometry depth profiling. Co-deposited films of Cu, Tb, and Mn show Cu emission around 530 nm instead of 420 nm due to coactivation by Mn.
Sol Particle Immunoassay (SPIA) (1980)

We describe the use of inorganic (metal) colloidal particles as a label for immunoassays. Dose-response curves for human placental lactogen (HPL) and human chorionic gonadotrophin (HCG) were obtained with sandwich immunoassays, using conjugates consisting of antibody-coated colloidal gold or silver particles. Several techniques were used to measure the amount of bound conjugate, viz. colorimetry and carbon rod atomic absorption spectrophotometry (CRAAS). At higher antigen concentrations the results of the assay could be read by the naked eye. Using gold particles as label and CRAAS as detection method, we found a detection limit for a sandwich HPL sol particle immunoassay (SPIA) of 1,4 pmol/l, which was equal to that of an optimalized competitive radioimmunoassay. When using a colorimeter the detection limit for HPL of this SPIA was 5,4 pmol/l, which was superior to that of a corresponding sandwich enzyme-immunoassay (EIA). HPL and HCG were also simultaneously determined, using microtitration plates, coated with a mixture of anti-HPL and anti-HCG, and a mixture of silver particle anti-HPL conjugate and gold particle anti-HCG conjugate. CRAAS was used to measure the bound amount of silver and gold conjugate. This simultaneous assay requires more work in order to obtain better sensitivities.
Comparative antilipidemic effects of various ethyl 5‐substituted benzofuran‐, 2,3‐dihydrobenzofuran‐, and 3(2H)‐benzofuranone‐2‐carboxylate analogs of clofibrate in a triton hyperlipidemic rat model (1976)

The antilipidemic properties of certain benzofuran-, 2,3-dihydrobenzofuran-, and 3(2H)-benzofuranone-2-carboxylate analogs of clofibrate in a hyperlipidemic rat model are described. The hyperlipidemia was induced by intraperitoneal injection of Triton WR-1339. The results were analyzed in light of structural modifications as well as the lipid solubility of substituted compounds as assessed by a consideration of calculated log P values. Comparisons are made between the activity of these compounds and the activity of related cyclic analogs previously reported. Among the various compounds tested, only the 5-C1 and phenylsybstituted dihydrobenzofurans were selective against elevated serum cholesterol levels in this animal model. The data presented support the hypothesis that the cholesterol and triglyceride lowering activity of clofibrate related analogs in this animal model may be separated through a consideration of log P, conformational, and electronic changes. The proposal is advanced that relatively minor structural modification of clofibrate related analogs may lead to compounds which are not only selective in the Triton model but also to compounds which are likely to exert their effects by differing modes of action.
Functional Characterization of Core Genes from Patients with Acute Hepatitis C Virus Infection (2010)

The data suggest that upon transmission, core quasispecies undergo genetic homogenization associated with amino acid changes that are rarely found in chronic infection and that, despite genetic variation, acute core isolates retain similar functions in vitro.
The Multiple Sclerosis Functional Composite measure (MSFC): an integrated approach to MS clinical outcome assessment (1999)

Clinical outcome assessment in Multiple Sclerosis (MS) is challenging due to the diversity and fluctuating nature of MS symptoms. Traditional clinical scales such as the EDSS are inadequate in their assessment of key clinical dimensions of MS (e.g., cognitive function), and they have psychometric limitations as well. Based on analyses of pooled data from natural history studies and from placebo groups in dinical trials, the National MS Society's clinical Outcomes Assessment Task Force recently proposed a new multidimensional clinical outcome measure, the MS Functional Composite (MSFC). The MSFC comprises quantitative functional measures of three key clinical dimensions of MS: leg functionl ambulation, arm/hand function, and cognitive function. Scores on component measures are converted to standard scores (z-scores), which are averaged to form a single MSFC score. Preliminary analyses confirm that: (I) the three clinical dimensions of the MSFC are relatively independent; (2) the MSFC is sensitive to clinical changes over I- and 2-year intervals; and (3) the MSFC has acceptable criterion validity (i.e., predicts both concurrent and subsequent EDSS change). The advantages and potential limitations of incorporating quantitative functional outcome measures such as the MSFC into collaborative databases are discussed.
Blast-Resistant Highway Bridges: Design and Detailing Guidelines (2010)

This report presents code-ready language containing general design guidance and a simplified design procedure for blast-resistant reinforced concrete bridge columns. The report also provides the results of experimental blast tests and analytical research on reinforced concrete bridge columns designed to investigate the effectiveness of a variety of different design techniques. The material in this report will be of immediate interest to bridge designers.
Serum Erythropoietin Levels in the Elderly (1991)

We evaluated the relationship between erythropoietin (EPO) and hemoglobin (Hb) concentrations in 156 normal subjects ranging from 60 to 98 years old. EPO was determined by a radioimmunoassay. The serum EPO concentration in subjects with Hb concentrations greater than 12.0 g/dl (26.9 +/- 15.2 mU/ml), was significantly higher than that in younger controls (15.8 +/- 5.0 mU/ml, p less than 0.001). No sex difference in serum EPO level was detected. In addition, there was an inverse semilogarithmic relationship between EPO and Hb concentrations in subjects with Hb concentrations less than 12.0 g/dl (r = -0.559, p less than 0.001). EPO concentrations in the elderly were lower than those in young subjects with iron deficiency anemia with the same Hb level. Thus, in the elderly, a high EPO concentration may be preventing a decrease in the Hb concentration. However, a decreased EPO response to low Hb concentrations may be a contributing factor in anemia in the elderly.
Commercial biotechnology processing thermal control for transfer payloads to/from the International Space Station (2000)

Biotechnology is undergoing a period of rapid and sustained growth, a trend which is expected to continue as the general population ages and as new medical treatments and products are conceived. As pharmaceutical and biomedical companies continue to search for improved methods of production and, for answers to basic research questions, they will seek out new avenues of research. Space processing on the International Space Station (ISS) offers such an opportunity! Space is rapidly becoming an industrial laboratory for biotechnology research and processing. Space bioprocessing offers exciting possibilities for developing new pharmaceuticals and medical treatments which can be used to benefit mankind on Earth. It also represents a new economic frontier for the private sector.