cssi/SciSciGPT-SciSciNet huggingface dataset:
Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response

Identification of functional non-coding variants and their mechanistic interpretation is a major challenge of modern genomics, especially for precision medicine. Transcription factor (TF) binding profiles and epigenomic landscapes in reference samples allow functional annotation of the genome, but do not provide ready answers regarding the effects of non-coding variants on phenotypes. A promising computational approach is to build models that predict TF-DNA binding from sequence, and use such models to score a variant’s impact on TF binding strength. Here, we asked if this mechanistic approach to variant interpretation can be combined with information on genotype-phenotype associations to discover transcription factors regulating phenotypic variation among individuals. We developed a statistical approach that integrates phenotype, genotype, gene expression, TF ChIP-seq, and Hi-C chromatin interaction data to answer this question. Using drug sensitivity of lymphoblastoid cell lines as the phenotype of interest, we tested if non-coding variants statistically linked to the phenotype are enriched for strong predicted impact on DNA binding strength of a TF and thus identified TFs regulating individual differences in the phenotype. Our approach relies on a new method for predicting variant impact on TF-DNA binding that uses a combination of biophysical modeling and machine learning. We report statistical and literature-based support for many of the TFs discovered here as regulators of drug response variation. We show that the use of mechanistically driven variant impact predictors can identify TF-drug associations that would otherwise be missed. We examined in depth one reported association—that of the transcription factor ELF1 with the drug doxorubicin—and identified several genes that may mediate this regulatory relationship. Our work represents initial steps in utilizing predictions of variant impact on TF binding sites for discovery of regulatory mechanisms underlying phenotypic variation. Future advances on this topic will be greatly beneficial to the reconstruction of phenotype-associated gene regulatory networks.
Teaching students effective practices for commenting computer source code: tutorial presentation

Tired of slogging through pages of printouts to grade student source code comments? Are your eyes burning from reading dense, unorganized, and unstructured comments? Are you thirsting in a desert of code bereft of comments explaining what the program does? Do your students feel like documentation is a waste of time and effort?
Predicting Mortality Risk in Patients with COVID-19 Using Artificial Intelligence to Help Medical Decision-Making

In the wake of COVID-19 disease, caused by the SARS-CoV-2 virus, we designed and developed a predictive model based on Artificial Intelligence (AI) and Machine Learning algorithms to determine the health risk and predict the mortality risk of patients with COVID-19. In this study, we used documented data of 117,000 patients world-wide with laboratory-confirmed COVID-19. This study proposes an AI model to help hospitals and medical facilities decide who needs to get attention first, who has higher priority to be hospitalized, triage patients when the system is overwhelmed by overcrowding, and eliminate delays in providing the necessary care. The results demonstrate 93% overall accuracy in predicting the mortality rate. We used several machine learning algorithms including Support Vector Machine (SVM), Artificial Neural Networks, Random Forest, Decision Tree, Logistic Regression, and K-Nearest Neighbor (KNN) to predict the mortality rate in patients with COVID-19. In this study, the most alarming symptoms and features were also identified. Finally, we used a separate dataset of COVID-19 patients to evaluate our developed model accuracy, and used confusion matrix to make an in-depth analysis of our classifiers and calculate the sensitivity and specificity of our model.
One-Year MRI Outcomes of Osteochondral Allograft Transplantation of the Knee for Large Chondral Defects: Comparison of Elliptical, Stacked, and Single Allografts:

Objectives:Osteochondral allograft transplantation (OCA) is a proven cartilage restoration procedure for patients with large chondral defects. However, elongated condylar lesions pose a challenge f...
History-driven modulations of population codes in early visual cortex during visual search

Abstract To find important objects, we must focus on our goals, ignore distractions, and take our changing environment into account. This is formalized in models of visual search whereby goal-driven, stimulus-driven and history-driven factors are integrated into a priority map that guides attention. History is invoked to explain behavioral effects that are neither wholly goal-driven nor stimulus-driven, but whether history likewise alters goal-driven and/or stimulus-driven signatures of neural priority is unknown. We measured fMRI responses in human visual cortex during a visual search task where trial history was manipulated (colors switched unpredictably or repeated). History had a near-constant impact on responses to singleton distractors, but not targets, from V1 through parietal cortex. In contrast, history-independent target enhancement was absent in V1 but increased across regions. Our data suggest that history does not alter goal-driven search templates, but rather modulates canonically stimulus-driven sensory responses to create a temporally-integrated representation of priority.
Synthesis and patterning of tunable multiscale materials with engineered cells

A major challenge in materials science is to create self-assembling, functional, and environmentally responsive materials which can be patterned across multiple length scales. Natural biological systems, such as biofilms, shells, and skeletal tissues, implement dynamic regulatory programs to assemble complex multiscale materials comprised of living and non-living components. Such systems can provide inspiration for the design of heterogeneous functional systems which integrate biotic and abiotic materials via hierarchical self-assembly. Here, we present a synthetic-biology platform for synthesizing and patterning self-assembled functional amyloid materials across multiple length scales with bacterial biofilms. We engineered Escherichia coli curli amyloid production under the tight control of synthetic regulatory circuits and interfaced amyloids with inorganic materials to create a biofilm-based electrical switch whose conductance can be selectively toggled by specific environmental signals. Furthermore, we externally tuned synthetic biofilms to build nanoscale amyloid biomaterials with different structure and composition through the controlled expression of their constituent subunits with artificial gene circuits. By using synthetic cell-cell communication, our engineered biofilms can also autonomously manufacture dynamic materials whose structure and composition change with time. In addition, we show that by combining subunit-level protein engineering, controlled genetic expression of self-assembling subunit proteins, and macroscale spatial gradients, synthetic biofilms can pattern protein biomaterials across multiple length scales. This work lays a foundation for synthesizing, patterning, and controlling composite materials with engineered biological systems. We envision that this approach can be expanded to other cellular and biomaterials contexts for the construction of self-organizing, environmentally responsive, and tunable multiscale composite materials with heterogeneous functionalities. Now published as: Nature Materials, doi:10.1038/nmat3912
Cough and dyspnea: Navigating the differential during a pandemic

Background Chronic Eosinophilic Pneumonia (CEP) is a rare disease of unknown etiology first described by Carinton et al. in 1969. It is characterized by an abnormal accumulation of eosinophils in the interstitium and alveolar spaces of the lung associated with bronchospasm and radiographic infiltrates. Case Presentation A 33-year-old female with GERD and allergic rhinitis presented to the ED with worsening dyspnea and non-productive cough following referral for pneumonia. Her initial symptoms occurred 5 months prior. She was since treated with levofloxacin twice for bronchial infections. Her symptoms worsened at night, with inhaled albuterol providing temporary relief. Travel history included air travel from Miami to New York every two weeks during the peak of the SARS-CoV2 pandemic and a hiking trip 1.5 years prior through mountains and caves in Arizona. Surgical history included silicone breast implants. She presented with an oral temperature of 99.8, a pulse of 108 bpm, and an oxygen saturation of 97% on RA. Physical exam demonstrated labored breathing and wheezing throughout both lung fields. Labs were notable for a leukocytosis of 13.4k with eosinophilia (35%), a negative SARS-CoV2 RNA nasopharyngeal swab, and an ESR of 35. CXR revealed multifocal bilateral patchy airspace opacities. CT chest revealed bilateral multifocal consolidated and ground glass opacities in a predominantly peripheral distribution. She underwent left robotic VATS and flexible bronchoscopy which revealed fibrosis, edema, enlarged mediastinal lymph nodes, and several mucopurulent plaques throughout the RLL and LLL. Pathology noted chronic eosinophilic organizing pneumonia. Treatment was initiated with intravenous steroids leading to dramatic clinical improvement, allowing prompt discharge on an oral tapering regimen. Upon outpatient two-week follow up, she reported significant improvement of her symptoms, with resolution of dyspnea and cough. Repeat CXR revealed resolution of all infiltrates. Discussion CEP often presents with progressive dyspnea, cough, bronchospasm, and low-grade fever. Eosinophilia and radiographic findings of peripheral consolidation are strongly suggestive of this diagnosis. As happens in 50% of cases of CEP, long term steroid dependency often becomes problematic, similar to cases of Bronchial Asthma. CEP is rare with an incidence of about 1/400,000 cases per year and can easily be misdiagnosed. In this particular case, COVID-19 was strongly suspected amongst an array of possible diagnoses;however, a thorough history along with strategic lab testing narrowed the differential. This case highlights the importance of maintaining a broad differential diagnosis especially in the setting of a global health crisis such as the SARS-CoV-2 pandemic.
Assessment of global health programs at accredited dental schools in the United States.

PURPOSE Oral diseases pose a serious global health challenge. As such, dental education must integrate global health with emphasis on scalable and sustainable solutions. The aim of our study was to capture the scope of global health programs offered to dental students in the United States and identify ways in which dental schools may modify their curricula to improve global health knowledge and accessibility for students. MATERIALS AND METHODS For this cross-sectional, cohort study, the investigators sent a confidential and electronic survey to 213 faculty members at the 67 accredited dental schools in the United States. This voluntary survey was distributed in September and October of 2020 with answers being self-reported. RESULTS A total of 40 different schools are represented in this study, representing 59.7% of accredited dental schools in the United States. Using descriptive statistics, the results present existing global health opportunities, barriers preventing schools from expanding global health education, and necessary resources that schools without a program need to establish one. CONCLUSION Our results demonstrate promising findings, in relation to global health being a vital part of dental education. However, there is an urgent need for enhanced and more structured education in this space. As the global burden of oral disease contributes to the degree and severity of noncommunicable diseases worldwide, the development of a sustainable, preventive primary care approach must integrate oral health, making future dental professionals a crucial component of global health.
Team Xc: JPL's collaborative design team for exploring CubeSat, NanoSat, and SmallSat-based mission concepts

Recently there has been an increasing demand for a rapid mission concept generation capability for CubeSats, NanoSats, and SmallSats at JPL and in the broader community in the Concept Maturity Level (CML) 2–5 range. To help address these needs, JPL's Innovation Foundry has extended its long-standing advanced concepts concurrent engineering team, Team X, with a new, agile, and collaborative design capability called Team Xc. This concurrent team-based approach provides rapid turnaround for small spacecraft mission and system early concept studies. The process is adaptable to a wide variety of CubeSat, NanoSat, and SmallSat customers and mission applications. Team Xc design and analysis services include feasibility assessments, trade space exploration studies, and point design studies, commensurate with the level of maturity of the mission concept. The team is assembled with experts experienced in designing, building, launching, and operating CubeSats; leaders in mission architecture, spacecraft design, and concurrent engineering methods; and subject matter experts tailored to the specific needs of each study and customer. The Team Xc capability has been applied to several studies and extended to cover a large breadth of missions spanning applications including Earth science, planetary science, astrophysics, and technology demonstration. Team Xc draws from Team X, JPL, and external subject matter experts to produce quick-turnaround reports targeted to each customer's needs.
Does Reductive Proof Theory Have A Viable Rationale

The goals of reduction andreductionism in the natural sciences are mainly explanatoryin character, while those inmathematics are primarily foundational.In contrast to global reductionistprograms which aim to reduce all ofmathematics to one supposedly ``universal'' system or foundational scheme, reductive proof theory pursues local reductions of one formal system to another which is more justified in some sense. In this direction, two specific rationales have been proposed as aims for reductive proof theory, the constructive consistency-proof rationale and the foundational reduction rationale. However, recent advances in proof theory force one to consider the viability of these rationales. Despite the genuine problems of foundational significance raised by that work, the paper concludes with a defense of reductive proof theory at a minimum as one of the principal means to lay out what rests on what in mathematics. In an extensive appendix to the paper,various reduction relations betweensystems are explained and compared, and arguments against proof-theoretic reduction as a ``good'' reducibilityrelation are taken up and rebutted.
A SEARCH FOR STAPES FOOTPLATE FIXATION IN AN INDIAN POPULATION, PREHISTORIC AND HISTORIC.

This study was made to find evidence of ear disease in ancient persons, special emphasis being placed upon otosclerosis with stapes footplate fixation, which would have suggested hearing loss during the life of the individual. Specimens examined were from Indian burials in South Dakota, consisting of skulls from persons ranging from birth to over 40 years. Two-hundred eleven of 221 were of sufficient age to have had stapedial fixation. Skull anomalies documented included exostoses in the auditory canals, benign bony tumors, evidence of ear infection, dental problems, evidence of trauma, and congenital defects. Despite long interment, some burials dating to about the time of Christ, skeletal details were well preserved. In all, 417 temporal bones from 221 skulls were examined. The ossicles were present as follows: malleus alone — 30; incus alone — 9; stapes alone — 5; multiple ossicles — 29. In 19 temporal bones the stapes was in the oval window (4.5%). There was no evidence of stapes footplate fixation. No congenital or developmental anomaly of the auditory ossicles was found. These results will be correlated with clinical studies now in progress on Indian reservations of South Dakota. The present Indians are descendents of those whose remnants have been studied.
In situ Raman analyses of deep-sea hydrothermal and cold seep systems (Gorda Ridge and Hydrate Ridge)

The Deep Ocean Raman In Situ Spectrometer (DORISS) instrument was deployed at the Sea Cliff Hydrothermal Field and Hydrate Ridge in July 2004. The first in situ Raman spectra of hydrothermal minerals, fluids, and bacterial mats were obtained. These spectra were analyzed and compared to laboratory Raman measurements of standards and samples collected from the site. Spectra of vent fluid (∼294°C at the orifice) at ∼2700 m depth were collected with noncontact and immersion sampling optics. Compared to spectra of ambient (∼2°C) seawater, the vent fluid spectra show changes in the intensity and positions of the water O-H stretch bands due to the elevated temperature. The sulfate band observed in seawater spectra is reduced in vent fluid spectra as sulfate is removed from vent fluid in the subseafloor. Additional components of hydrothermal fluid are present in concentrations too low to be detected with the current Raman system. A precision underwater positioner (PUP) was used to focus the laser spot on opaque samples such as minerals and bacterial mats. Spectra were obtained of anhydrite from actively venting chimneys, and of barite deposits in hydrothermal crusts. Laboratory analysis of rock samples collected in the vent field also detected the presence of gypsum. Spectra of bacterial mats revealed the presence of elemental sulfur (S8) and the carotenoid beta-carotene. Challenges encountered include strong fluorescence from minerals and organics and insufficient sensitivity of the instrument. The next generation DORISS instrument addresses some of these challenges and holds great potential for use in deep-sea vent environments.
Studies in the diabetic mutant mouse. II. Electron microscopy of pancreatic islets.

Electronmicroscopic studies were performed on the pancreatic islets of normal mice (C 57BL/ KsJ) and of diabetic mutants (C 57 BL/Ks-db/db) at all stages of the syndrome. The ultrastructural appearance of the islets of prehyperglycemic mutants (Blood Glucose < 120 mg/100 ml) did not differ from that of normal mice. The two could not be differentiated without the aid of radioautography, which demonstrated that the beta cells of prehyperglycemic mutants incorporated thymidine-3H with greater frequency. Beta cells of early hyperglycemic mice (BG 130–200 mg/100 ml) revealed partial secretory degranulation, increased quantities of rough endoplasmic reticulum and enlarged Golgi structures. Beta cell necrosis was most common in mice with established hyperglycemia during the period of most rapid blood glucose elevation. It negated the effects of the short lived increase in beta cell proliferation and was eventually responsible for a reduction in beta cell mass and relative insulin insufficiency. The presence of unique intra-islet ductal structures and acinar cells later in the syndrome is unknown in other diabetic models. The proliferating ductal epithelial cells presumably gave rise to ciliated cells, mucous goblet or Paneth cells and pancreatic acinar cells, but no evidence of beta cell neogenesis was obtained. “Virus-like” particles were identified within intact and necrotic beta cells and intra-islet acinar cells.
Advances in Solid State Lasers at NASA Langley Research Center

An overview of NASA's vision for 21st Century using space-based solid-state lasers for Earth observations was presented. Current and future usage of lasers for observing Earth processes, such as climate systems caused by man-induced forces upon the environment were highlighted. For some projects mission details and measurements systems using lasers were discussed, covering also the laser systems development processes.
Synthesis of chondroitin sulfate by the human cervix during the menstrual cycle.

Abstract 1.1. The rate of S 35 uptake by the human cervix in vitro was measured as an indication of the chondroitin sulfate synthesis in the ground substance of this tissue. 2.2. Rates of S 35 uptake were high in specimens removed during the proliferative phase of the normal menstrual cycle. 3.3. Rates of S 35 uptake were low during the secretory phase of the cycle in an inverse relationship to presumed progesterone production by the corpus luteum. 4.4. Some estrogen secretion was necessary for elevated S 35 uptake. Low uptake rates were observed in specimens from patients with atrophic endometria. 5.5. Similarities between these findings and studies by others on cervical dilatation and effacement during the normal menstrual cycle are discussed.
Increased excitability and excitatory synaptic transmission during in vitro ischemia in the neonatal mouse hippocampus.

Abstract Objective: The present study tested the hypothesis that exposure to in vitro hypoxia–ischemia alters membrane properties and excitability as well as excitatory synaptic transmission of CA1 pyramidal neurons in the neonatal mouse. Methods: Experiments were conducted in hippocampal slices in P7–P9 C57Bl/6 mice using whole-cell patch clamp in current- and voltage-clamp mode. Passive membrane potential (Vm), input resistance (Rin) and active (action potential (AP) threshold and amplitude) membrane properties of CA1 pyramidal neurons were assessed at baseline, during 10 min in vitro ischemia (oxygen-glucose deprivation (OGD)) and during reoxygenation. Spontaneous and miniature excitatory post-synaptic currents (s and mEPSCs) were studied under similar conditions. Results: OGD caused significant depolarization of CA1 pyramidal neurons as well as decrease in AP threshold and increase in AP amplitude. These changes were blocked by the application of tetrodotoxin (TTX), indicating Na+ channels’ involvement. Following 10 min of reoxygenation, significant membrane hyperpolarization was noted and it was associated with a decrease in Rin. AP threshold and amplitude returned to baseline during that stage. sEPSC and mEPSC frequency increased during both OGD and reoxygenation but their amplitude remained unchanged. Additionally, we found that OGD decreases Ih (hyperpolarization activated current) in CA1 neurons from neonatal mice and this effect persists during reoxygenation. Significance: These results indicate that in vitro ischemia leads to changes in membrane excitability mediated by sodium and potassium channels. Further, it results in enhanced neurotransmitter release from presynaptic terminals. These changes are likely to represent one of the mechanisms of hypoxia/ischemia-mediated seizures in the neonatal period.
Using Dynamic Rewards to Learn a Fully Holonomic Bipedal Walk

This paper presents the design and learning architecture for a fully holonomic omnidirectional walk used by the UT Austin Villa humanoid robot soccer agent acting in the RoboCup 3D simulation environment. By“fully holonomic” we mean the walk allows for movement in all directions with equal velocity. The walk is based on a double linear inverted pendulum model and was originally designed for the actual physical Nao robot. Parameters for the walk are optimized for maximum speed and stability while at the same time a novel approach of reweighting rewards for walking speeds in the cardinal directions of forwards, backwards, and sideways is utilized to promote equal walking velocities in all directions. A variant of this walk which uses the same walk engine, but is not fully holonomic as it employs three different sets of learned walk parameters biased toward maximizing forward walking speed, was the crucial component in the UT Austin Villa team winning the 2011 RoboCup 3D simulation competition. Detailed experiments reveal that adaptively changing the weights of rewards over time is an effective method for learning a fully holonomic walk. Additional data shows that a team of agents using this learned fully holonomic walk is able to beat other teams, including that of the 2011 RoboCup 3D simulation champion UT Austin Villa team, that utilize non-fully holonomic walks.
Use of Forces from Instrumented Charpy V-Notch Testing to Determine Crack-Arrest Toughness

The objective of this investigation is an estimation of the crack-arrest toughness, particularly of irradiated materials, from voltage versus time output of an instrumented setup during a test on a Charpy V-notch (CVN) specimen. This voltage versus time trace (which can be converted to force versus displacement) displays events during fracture of the specimen. Various stages of the fracture process can be identified on the trace, including an arrest point indicating arrest of brittle fracture. The force at arrest, F{sub a}, versus test temperature, T, relationship is examined to explore possible relationships to other experimental measures of crack-arrest toughness such as the drop-weight nil-ductility temperature (NDT), or crack-arrest toughness, K{sub a}. For a wide range of weld and plate materials, the temperature at which F{sub a} = 2.45 kN correlates with NDT with a standard deviation, sigma, of about 11 K. Excluding the so-called low upper-shelf energy (USE) welds from the analysis resulted in F{sub a} = 4.12 kN and {sigma} = 6.6 K. The estimates of the correlation of the temperature for F{sub a} = 7.4 kN with the temperature at 100-MPa{radical}m level for a mean American Society of Mechanical Engineers (ASME) type K{sub Ia} curve through crack-arrest toughnessmore » values show that prediction of conservative values of K{sub a} are possible.« less
Mammary intraepithelial neoplasia outgrowths (MINO): MINO and human ductal carcinoma in situ

Mouse models of human mammary intraepithelial neoplasia have been described in a number of contexts. In general, descriptions of early stages of progression in genetically engineered mice that go on to develop invasive and even metastatic carcinomas are compared with human ductal carcinoma in situ (DCIS). In some instances, lesions with phenotypic similarity to human DCIS are compared, even without evidence of progression. The terminology for these processes in the mouse mammary gland requires precise definition. Otherwise, it is impossible to compare the variety of available models for study utility. Experimentally driven operational definitions are optimal. We have studied a series of transplantable mammary intraepithelial neoplasia outgrowths (MINOs) derived from the transgenic mouse mammary tumor virus promoter-driven polyoma virus middle T oncogene FVB mice. We have characterized their behavior experimentally and morphologically. Experimentally, these MINOs meet the most stringent criteria to be considered premalignant. They are capable of orthotopic growth in the gland cleared mammary fat pad, are without being capable of ectopic (subcutaneous) growth, and have a consistent transformation to the fully malignant behavior (capable of ectopic growth)–defined therefore as invasive carcinoma. Morphologically, there is a high degree of heterogeneity both within and between individual MINO lines. Nevertheless, all consistently transform to behaviorally and morphologically similar carcinomas. MINOs therefore compare closely with human DCIS. Human DCIS is similarly defined by its universal potential (if incompletely treated) to progress to invasive carcinoma, despite heterogeneity within a given breast or between individual patients. We extend the comparison using immunophenotypic analysis, and gene expression analysis. Overall, our goal is to better model human DCIS, in a reproducible and robust mouse model system suitable for interventional studies. By creating a serially transplantable series of MINOs we have removed much of the variability which would otherwise confound such study. Derivation of MINOs from a variety of genetically engineered mice backgrounds may provide additional critical reagents for the preclinical study of DCIS.
Testing the reverse transcriptase model of somatic mutation

Somatic hypermutation of the variable (V) regions of rearranged immunoglobulin genes leads to antibody affinity maturation. Although this process has been extensively studied, the mechanisms responsible for these multiple point mutations are still elusive. One mechanism that was proposed over 10 years ago by Steele and Pollard was that an intrinsic reverse transcriptase (RT) copies the nascent mRNA creating the large number of observed point mutations due to its high error rate. A cDNA copy of the mutated V region would then replace the endogenous DNA through a gene conversion-like event, thus integrating these point mutations into the genome. This model of hypermutation would account for the very high mutation rate, the presence of hotspots, strand bias, the requirement for transcription and localization of mutation within the immunoglobulin V region. Using AZT and ddC to inhibit endogenous RTs, we have assayed for somatic mutation using a murine in vivo model. Somatic mutation occurred at similar frequencies and with the same characteristics with or without treatment of RT inhibitors, suggesting that standard reverse transcription is not required for antibody V region hypermutation in the mouse.
Molecular dynamics and thermodynamics of protein-RNA interactions: mutation of a conserved aromatic residue modifies stacking interactions and structural adaptation in the U1A-stem loop 2 RNA complex.

Molecular dynamics (MD) simulations and free energy component analysis have been performed to evaluate the molecular origins of the 5.5 kcal/mol destabilization of the complex formed between the N-terminal RNP domain of U1A and stem loop 2 of U1 snRNA upon mutation of a conserved aromatic residue, Phe56, to Ala. MD simulations, including counterions and water, have been carried out on the wild type and Phe56Ala peptide-stem loop 2 RNA complexes, the free wild type and Phe56Ala peptides, and the free stem loop 2 RNA. The MD structure of the Phe56Ala−stem loop 2 complex is similar to that of the wild type complex except the stacking interaction between Phe56 and A6 of stem loop 2 is absent and loop 3 of the peptide is more dynamic. However, the MD simulations predict large changes in the structure and dynamics of helix C and increased dynamic range of loop 3 for the free Phe56Ala peptide compared to the wild type peptide. Since helix C and loop 3 are highly variable regions of RNP domains, this indicates th...
Probable correctness theory

Abstract A theory of ‘probable correctness’ is proposed to assess the reliability of software through testing. Current research in testing is not adequate for this assessment. Most testing methods are intended for debugging, to find failures and connect them to program faults for repair. When these methods no longer expose errors, no analysis has been done to find the confidence that may be placed in the software. (Preliminary results here are that this confidence should be low.) Other work applies conventional decision theory to inputs as samples of a program's use. The application is suspect because the necessary independence and distribution assumpions may be violated; in any case, the results are intuitively incorrect. The proposed theory relies on a uniform distribution of test samples, but relates these to textually occurring faults. Preliminary results include an analysis of partition testing, and suggestions for textual sampling. It is crucial that any such confidence theory be plausible, so the foundations of program sampling are examined in detail.
Three-dimensional computed tomography analysis of airway volume changes after rapid maxillary expansion.

Introduction In this retrospective study with 3-dimensional computed tomography, we evaluated airway volume, soft-palate area, and soft-tissue thickness changes before and after rapid maxillary expansion in adolescents. Another purpose was to determine whether rapid maxillary expansion caused changes in the palatal and mandibular planes and facial height. Methods The sample comprised 20 patients who were treated with rapid maxillary expansion. Spiral tomographs were taken before and 3 months after treatment. Reliability studies were performed, and then volumetric, soft-palate area, soft-tissue thickness, and cephalometric parameters were compared on the tomographs. Intraclass correlations were performed on the reliability measurements. Before and after rapid maxillary expansion measurements were compared by using Wilcoxon signed rank tests. Spearman correlation coefficients were used to evaluate the associations among the airway volume, soft-palate area, soft-tissue thickness, and cephalometric measurements. Significance was accepted at P ≤0.05 for all tests. Results Intraclass correlation coefficients were ≥0.90 for all reliability measures. Significant increases from before to after rapid maxillary expansion were found in nasal cavity and nasopharynx volumes, and for the measurements of MP-SN, S-PNS, N-ANS, ANS-Me, and N-Me. Significant positive correlations existed between changes in PP-SN and N-ANS, and ANS-Me and N-Me. Conclusions Rapid maxillary expansion causes significant increases in nasal cavity volume, nasopharynx volume, anterior and posterior facial heights, and palatal and mandibular planes.
Recurrences for sums of powers of binomial coefficients

Abstract Define S(r)n=∑nk=0(nk)r(r=1,2,…). An elementary method is given for finding a recurrence for Sn(r) with [ (r+3) 2 ] terms. This confirms an 1895 conjecture of Franel.
A dopaminergic basis for the effects of amphetamine on a mouse "preadolescent hyperkinetic" model.

Abstract Amphetamine significantly attenuated neural excitation, which was indexed by the onset of a myoclonic seizure, in young mice genetically predisposed to high levels of neural excitation and motor activity, whereas it increased excitation in mature mice of the same genetic stock. Apomorphine simulated the effects of amphetamine while clonidine did not. Consequently, it appears that a dopaminergic mechanism, which subsequently undergoes a developmental alteration, is mediating the paradoxical antiexcitatory effect of amphetamine.
A neural networks approach to image data compression

We present a novel neural model for image compression called the direct classification (DC) model. The DC is a hybrid between a subset of the self-organizing Kohonen (SOK) model and the adaptive resonance theory (ART) model. The DC is a fast and efficient neural classification engine. The DC training utilizes the accuracy of the winner-takes-all feature of the SOK model and the elasticity/speed of the ART1 model. The DC engine has experimentally achieved much better results than the state-of-the-art peer image compression techniques (e.g., JPEG2000 and DjVu wavelet technology) especially in the domains of colored documents and still satellite images. We include a comprehensive analysis of the most important parameters of our DC system and their effects on system performance.
Storage stability of poultry fat and diesel fuel mixtures: Specific gravity and viscosity

Poultry fat (biofuel) and its 20%, 40%, 60% and 80% mixtures with #2 pump diesel fuel were stored for 1 year at bench scale (1 L) under controlled laboratory conditions at 4, 38, 54.4 °C and at ambient room temperature. Poultry fat (100%) was studied under these same conditions with and without an antioxidant additive. Poultry fat mixtures (20% and 80%) were also stored at pilot scale (250 gallons) under outdoor, ambient conditions. Physical properties and phenomenon relevant to the use of these mixtures as biofuels for industrial boilers were studied and tracked. These properties include specific gravity, dynamic viscosity, sedimentation accumulation and separation (layering). Corrosive effects of these fuels on various metals were also examined. Viscosity and specific gravity of these biofuels changed very little over the course of the 1 year storage period. Sediment accumulation was present in all treatments, with increasing sedimentation correlating with increasing biofuel concentrations. The addition of antioxidant to 100% biofuel minimized changes in physical properties and sedimentation over the course of this study. Layering occurred in all mixtures of poultry fat and diesel fuel. Results also include the approximate amount of energy required to insure proper mixing of each treatment. After mixing, homogenization was maintained for considerable time periods. This suggests that mixing should only be performed immediately before the fuels are utilized. Corrosive properties of these biofuels were generally as expected; brass and copper were susceptible to attack by these fuels where as 316 stainless steel and carbon steel were not.
Desmosterol as a common intermediate in the conversion of a number of C28 and C29 plant sterols to cholesterol by the tobacco hornworm.

Manduca sexta (Johannson) est capable de transformer 7 phytosterols en cholesterol. Ainsi, cet insecte peut dealcoyler le α- et leβ-methyl de meme que les groupes methylene et ethylidenes du carbone 24 et peut hydrogener la double liaison 22, 23. Quand ces sterols sont combines au 20, 25-diazacholesterol, on a constate dans tous les cas que la transformation en cholesterol s'effectue par l'intermediaire commun, le desmosterol.
The pharmacokinetics of aminoguanidine in end-stage renal disease patients on hemodialysis☆

Aminoguanidine is an investigational agent that may slow or prevent many diabetes-related complications. Since the elimination of aminoguanidine is dependent on renal function, its pharmacokinetics was investigated in eight chronic renal failure patients maintained on hemodialysis. Each patient received 300 mg of aminoguanidine hydrochloride during both an interdialytic and an intradialytic period. During the interdialytic period, the maximum aminoguanidine concentration (Cmax) and time to reach Cmax was 4.5 micrograms/mL and 1.5 hours, respectively. The terminal elimination half-life in these patients was prolonged (37.9 hours). The renal clearance was 2.1 mL/min. Only 8.7% of the administered dose was recovered unchanged in the urine, which is markedly reduced from what is recovered in urine in subjects with normal renal function. There was a positive correlation between the renal clearance of aminoguanidine and the patients' residual renal function (P < 0.05). During hemodialysis, the half-life of aminoguanidine was shortened to 3.9 hours. The hemodialysis clearance of aminoguanidine was 203.6 mL/min. After cessation of hemodialysis, a significant rebound in plasma aminoguanidine concentrations (mean, 39%) was observed. Thus, the dose of aminoguanidine hydrochloride will need to be significantly reduced in patients with end-stage renal disease. Given the interdialytic and intradialytic pharmacokinetics of aminoguanidine, three times weekly dosing after each hemodialysis session is suggested.
Electrochemical oxidation of Mo(CO)4(LL) and Mo(CO)3(LL)(CH3CN): Generation, infrared characterization, and reactivity of [Mo(CO)4(LL)]+ and [Mo(CO)3(LL)(CH3CN)]+ (LL = 2,2′-bipyridine, 1,10-phenanthroline and related ligands)

Abstract Mo(CO) 4 (LL) complexes, where LL = polypyridyl ligands such as 2,2′-bipyridine and 1,10-phenanthroline, undergo quasi-reversible, one-electron oxidations in methylene chloride yielding the corresponding radical cations, [Mo(CO) 4 (LL)] + . These electrogenerated species undergo rapid ligand substitution in the presence of acetonitrile, yielding [Mo(CO) 3 (LL)(CH 3 CN)] + ; rate constants for these substitutions were measured using chronocoulometry and were found to be influenced by the steric and electronic properties of the polypyridyl ligands. [Mo(CO) 3 (LL)(CH 3 CN)] + radical cations, which could also be generated by reversible oxidation of Mo(CO) 3 (LL)(CH 3 CN) in acetonitrile, can be irreversibly oxidized yielding [Mo(CO) 3 (LL)(CH 3 CN) 2 ] 2+ after coordination by an additional acetonitrile. Infrared spectroelectrochemical experiments indicate the radical cations undergo ligand-induced net disproportionations that follow first-order kinetics in acetonitrile, ultimately yielding the corresponding Mo(CO) 4 (LL) and [Mo(CO) 2 (LL)(CH 3 CN) 3 ] 2+ species. Rate constants for the net disproportionation of [Mo(CO) 3 (LL)(CH 3 CN)] + and the carbonyl substitution reaction of [Mo(CO) 3 (LL)(CH 3 CN) 2 ] 2+ were measured. Thin-layer bulk oxidation studies also provided infrared characterization data of [Mo(CO) 4 (ncp)] + (ncp = neocuproine), [Mo(CO) 3 (LL)(CH 3 CN)] + , [Mo(CO) 3 (LL)(CH 3 CN) 2 ] 2+ and [Mo(CO) 2 (LL)(CH 3 CN) 3 ] 2+ complexes.
The enthalpies of formation of MgAl2O4, MgSiO3, Mg2SiO4 and Al2SiO5 by oxide melt solution calorimetry

Abstract In this communication we report new values of the enthalpy of formation from the oxides of MgAl 2 O 4 (spinel), MgSiO 3 (pyroxene), Mg 2 SiO 4 (olivine), Al 2 SiO 5 (kyanite) and Al 2 SiO 5 (sillimanite) obtained by oxide melt solution calorimetry at 965 K and 1173 K. The standard enthalpies of formation at 298 K are calculated from the 965 K data and are compared with corresponding values in the literature.
Mueller matrix ellipsometry with imperfect compensators

We describe the use of an ellipsometer having the configuration PCSC’A to determine the Mueller matrix of a linear optical system S, using imperfect compensators C and C′ and linear polarizer P and analyzer A. Two manual (16 intensity), one semiautomatic (rotating-compensator) and one fully automatic (dual rotating-compensator) methods are described. Real-time Fourier analysis (of both raw and reduced data) is used in the automatic methods to reduce random and systematic measurement errors. Calibration procedures given for each method permit Mueller matrix spectroscopy using (quasi-) achromatic retarders whose principal axes, as well as retardation and transmission ratios change slightly with wavelength.
Mitotic recombination within the centromere of a yeast chromosome

Centromeres are the structural elements of eukaryotic chromosomes that hold sister chromatids together and to which spindle tubules connect during cell division. Centromeres have been shown to suppress meiotic recombination in some systems. In this study yeast strains genetically marked within and flanking a centromere, were used to demonstrate that gene conversion (nonreciprocal recombination) tracts in mitosis can enter into and extend through the centromere.
Exposures of preschool children to chlorpyrifos, diazinon, pentachlorophenol, and 2,4-dichlorophenoxyacetic acid over 3 years from 2003 to 2005: A longitudinal model

The impact of the US EPA-required phase-outs starting in 2000-2001 of residential uses of the organophosphate (OP) pesticides chlorpyrifos (CPF) and diazinon (DZN) on preschool children's pesticide exposures was investigated over 2003-2005, in the Raleigh-Durham-Chapel Hill area of North Carolina. Data were collected from 50 homes, each with a child initially of age 3 years (OCh) and a younger child (YCh). Environmental samples (indoor and outdoor air, dust, soil) and child-specific samples (hand surface residue, urine, diet) were collected annually over 24-h periods at each home. Child time-activity diaries and household pesticide use information were also collected. Analytes included CPF and DZN; pentachlorophenol (PCP); 2,4-dichlorophenoxyacetic acid (2,4-D); the CPF metabolite 3,5,6-trichloro-2-pyridinol (TCP); and the DZN metabolite 2-isopropyl-6-methyl-4-pyrimidinol (IMP). Exposures (ng/day) through the inhalation, dietary ingestion, and indirect ingestion were calculated. Aggregate potential doses in ng/kg body weight per day (ng/kg/day) were obtained by summing the potential doses through the three routes of exposure. Geometric mean aggregate potential doses decreased from 2003 to 2005 for both OCh and YCh, with the exception of 2,4-D. Child-specific longitudinal modeling indicated significant declines across time of the potential doses of CPF, DZN, and PCP for both children; declines of IMP for both children, significant only for OCh; a decline of TCP for OCh but an increase of TCP for YCh; and no significant change of 2,4-D for either child. Age-adjusted modeling indicated significant effects of the child's age for all except CPF, and of time for all except PCP and 2,4-D. Within-home variability was small compared with that between homes; variability was smallest for 2,4-D, both within and between homes. The aggregate potential doses of CPF and DZN were well below published reference dose values. These findings show the success of the US EPA restrictions in reducing young children's pesticide exposures.
Étude Expérimentale du Déterminisme de la Régénération des Nageoires Chez les Poissons Téléostéens

Abstract Jacqueline Buser-Lahaye. Annales de l'Institut Oceanographique (Monaco), nouvelle serie, tome 28, fascicule 1, 61 pp., 25 figs., 19 tables. Paris, Masson et Cie., 1953.
Synthesis and cationic photopolymerization of alkoxyallene monomers

A series of cationically polymerizable mono-and difunctional alkoxyallene monomers have been prepared via the straight forward base catalyzed isomerization of the corresponding propargyl ethers. Rate studies conducted using real-time infrared spectroscopy showed that these monomers exhibit high reactivity in photoinitiated cationic polymerization. Monomers bearing a single alkoxyallene group undergo rapid polymerization to yield crosslinked polymers indicating that both double bonds react during polymerization. A mechanism has been proposed that explains this observation. © 1995 John Wiley & Sons, Inc.
Physical activity of Canadian and American children: a focus on youth in Amish, Mennonite, and modern cultures.

Childhood obesity is an urgent public health problem in North America and throughout most of the industrialized world. Diminishing levels of physical activity and the growth of sedentary pursuits m...
Effects of Age, Adaptive Behavior, and Cognitive Abilities on Competence-Related Abilities in Children and Adolescents

Consideration of competence to waive Miranda rights (CWM) and competence to stand trial (CST) has become commonplace in the juvenile justice system. Past research has shown age and intelligence are important risk factors for incompetence, but investigations of particular aspects of cognition and more practical aspects of functioning are limited. The present study investigated the direct and indirect effects of age, adaptive functioning, and three specific cognitive abilities (working memory, attention, and processing speed) on both types of competence for 92 children and adolescents ages 8–16. While age was strongly related to all aspects of both types of competence, mixed results were found for the cognitive abilities, and adaptive functioning was only related to some aspects of CWM. Contrary to expectations, it was found that, for the most part, the effect cognitive abilities had on competence did not vary depending on the age of the child or adolescent, and that higher adaptive functioning did not serv...
A novel predictor–corrector algorithm for sub‐structure pseudo‐dynamic testing

A new predictor-corrector (P-C) method for multi-site sub-structure pseudo-dynamic (PSD) test is proposed. This method is a mixed time integration method in which computational components separable from experimental components are solved by implicit time integration method (Newmark β method). The experiments are performed quasi-statically based on explicit prediction of displacement. The proposed P-C method has an important advantage as it does not require the determination of the initial stiffness values of experimental components and is thus suitable for representing elastic and inelastic systems. A parameter relating to quality of displacement prediction at boundaries nodes is introduced. This parameter is determined such that P-C method can be applicable to many practical problems. Error-propagation characteristics of P-C method are also presented. A series of examples including linear and non-linear soil-foundation-structure interaction problem demonstrate the performance of the proposed method.