cssi/SciSciGPT-SciSciNet huggingface dataset:
Racial/ethnic group differences in parenting attitudes among at-risk emerging adults: The roles of adversity, relationship quality, and caregiver involvement and attitudes.

Abstract Background Healthy parenting attitudes are foundational for positive parenting and child well-being. However, few studies explore their formation and mediators explaining racial/ethnic group differences. Objective The present study prospectively examines potential mediators for racial/ethnic group differences in parenting attitudes in a diverse sample of emerging adults (EA). Participants & setting Participants are EA and their caregivers (N = 891) who participated in the Longitudinal Studies of Child Abuse and Neglect (LONGSCAN). Methods Adverse childhood experiences (ACEs), parenting attitudes, and caregiver-child relationship quality and involvement were assessed. Mediators of racial/ethnic group differences were tested using Structural Equation Modeling with bias-corrected confidence intervals based on 1000 bootstrapped samples. Results Black EA had less appropriate developmental expectations and perceptions of family roles, empathy toward children, and rejection of physical punishment, compared to White EA. Latinx EA also had less empathy toward children compared to White EA. Caregivers’ parenting attitudes mediated group differences, beyond ACEs and relationship quality and involvement. Significant mediation effects include: appropriate developmental expectations, R2 = 0.08, p Conclusion Findings highlight the mediating role of intergenerational transmission of parenting attitudes for explaining racial-ethnic differences and supporting positive parenting practices in diverse communities.
An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2.

Summary Soluble forms of angiotensin-converting enzyme 2 (ACE2) have recently been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We report on an improved soluble ACE2, termed a "microbody," in which the ACE2 ectodomain is fused to Fc domain 3 of the immunoglobulin (Ig) heavy chain. The protein is smaller than previously described ACE2-Ig Fc fusion proteins and contains an H345A mutation in the ACE2 catalytic active site that inactivates the enzyme without reducing its affinity for the SARS-CoV-2 spike. The disulfide-bonded ACE2 microbody protein inhibits entry of SARS-CoV-2 spike protein pseudotyped virus and replication of live SARS-CoV-2 in vitro and in a mouse model. Its potency is 10-fold higher than soluble ACE2, and it can act after virus bound to the cell. The microbody inhibits the entry of β coronaviruses and virus with the variant D614G spike. The ACE2 microbody may be a valuable therapeutic for coronavirus disease 2019 (COVID-19) that is active against viral variants and future coronaviruses.
Spike-Associated Networks Predict Postsurgical Outcomes in Children With Refractory Epilepsy.

PURPOSE Up to half of the children undergoing epilepsy surgery will continue to have seizures (szs) despite a cortical resection or ablation. Functional connectivity has shown promise in better identifying the epileptogenic zone. We hypothesized that cortical areas showing high information outflow during interictal epileptiform discharges are part of the epileptogenic zone. METHODS We identified 22 children with focal epilepsy who had undergone stereo electroencephalography, surgical resection or ablation, and had ≥1 year of postsurgical follow-up. The mean phase slope index, a directed measure of functional connectivity, was calculated for each electrode contact during interictal epileptiform discharges. The positive predictive value and negative predictive value for a sz-free outcome were calculated based on whether high information outflow brain regions were resected. RESULTS Resection of high outflow (z-score ≥ 1) and very high outflow (z-score ≥ 2) electrode contacts was associated with higher sz freedom (high outflow: χ2 statistic = 59.1; P < 0.001; very high outflow: χ2 statistic = 31.3; P < 0.001). The positive predictive value and negative predictive value for sz freedom based on resection at the electrode level increased at higher z-score thresholds with a peak positive predictive value of 0.86 and a peak negative predictive value of 0.9. CONCLUSIONS Better identification of the epileptogenic zone has the potential to improve epilepsy surgery outcomes. If the surgical plan can be modified to include these very high outflow areas, more children might achieve sz freedom. Conversely, if deficits from resecting these areas are unacceptable, ineffective surgeries could be avoided and alternative therapies offered.
Crystal Truncation Rod as a Convolution of Three-Dimensional Bravais Lattice with X-Ray Reflectivity

An expression for crystal truncation rod intensity is derived from a convolution of three dimensional Bravais lattice with x-ray reflectivity. For mosaic blocks with no miscut surface the expression recovers Robinson’s result. For the mosaic blocks with miscuts, the expression is reduced to Andrews and Cowley’s form.
Tripeptides on Gold Nanoparticles: Structural Differences between Two Reverse Sequences as Determined by Solid-State NMR and DFT Calculations.

The reverse-sequence peptides CysAlaAla and AlaAlaCys may attach to gold nanoparticles through the thiol group, and they differ primarily by whether the charged amino or the carboxylate group is proximal to the sulfur. Alanine residues in these peptides are not expected to interact significantly with the gold surface and serve to place a large separation between the amino and carboxylate groups. Solid-state NMR experiments and DFT calculations were performed to explore the structural differences between CysAlaAla on gold nanoparticles and AlaAlaCys on gold nanoparticles. It is found that the relative positions between the thiol, amino, and carboxylate groups strongly influences the structures of the peptide–gold systems. CysAlaAla orients parallel to the gold surface in a monolayer fashion, whereas AlaAlaCys forms an interdigitating bilayer-like structure that is oriented upright relative to the gold surface.
Motion control for underactuated mechanical systems on lie groups

Control design for underactuated mechanical systems is an active area of research. In this paper we focus on mechanical control systems defined on Lie groups with the Lagrangian equal to kinetic energy. Examples include satellites and underwater vehicles. Under a controllability-assumption, we propose two algorithms to compute small amplitude, periodic inputs that achieve arbitrary reconfigurations.
The use of high positive end-expiratory pressure for respiratory failure in abdominal compartment syndrome.

We report a case in which a non-trauma patient suffering hematemesis and undergoing massive volume resuscitation developed abdominal compartment syndrome (ACS). The abdominal distension severely compromised his pulmonary functioning: a chest radiograph showed low lung volumes and dense bilateral parenchymal opacities. His blood oxygen saturation reached as low as 32%. Because he was hemodynamically unstable and coagulopathic, decompressive surgery was not possible. We gradually raised the ventilator settings to reinflate the lungs (positive end-expiratory pressure [PEEP] was raised to 50 cm H 2 O, peak inspiratory pressure to 100 cm H 2 O, and plateau inspiratory pressure to 80 cm H 2 O) and continued fluid resuscitation, and within an hour his blood oxygen saturation increased to 100%. In this case high PEEP was beneficial in a situation in which decompressive surgery was not feasible, but we do not suggest that high PEEP necessarily improves survival or that high PEEP is better than surgical decompression. On the contrary, high-pressure ventilation can be harmful in the setting of acute lung injury and acute respiratory distress syndrome, so we do not advocate high PEEP for all patients with hypoxemia and ACS, especially considering that many of the conditions associated with ACS can also precipitate acute lung injury and acute respiratory distress syndrome. As well, high-pressure ventilation can increase the risk of hypotension by impairing venous return. However, our case suggests that high PEEP may temporize in certain situations in which ACS causes life-threatening hypoxia but surgical decompression is not possible.
Rapid Quantitative Method for Salmonella Detection in Polluted Waters

A procedure has been developed for the enumeration of salmonellae in polluted waters using several modifications of existing techniques. Confirmation of salmonellae is achieved within 48 hr. This procedure includes selective enrichment in m-Tetrathionate Broth (22 ± 1 hr), plating on Brilliant Green Sulfa Agar (20 ± 1 hr), and confirmation by flagellar (H) agglutination of the growth in a mannosecontaining medium (6 ± 1 hr). An incubation temperature of 41.5 C was used throughout this procedure. Dilution to extinction techniques (most probable number) were employed to enumerate salmonellae. Large sample volumes were concentrated through the use of membrane filters. This technique proved to be rapid and reliable for the enumeration of salmonellae in water, waste water, and waste-water sludges.
The Sialic Acids XII. SYNTHESIS OF COLOMINIC ACID BY A SIALYLTRANSFERASE FROM ESCHERICHIA COLI K-235

Abstract Partial purification of an Escherichia coli sialyltransferase (CMP-N-acetylneuraminic acid-colominic acid sialyltransferase) that transfers N-acetylneuraminic acid (N-AN) from cytidine 5'-monophospho-N-acetylneuraminic acid to colominic acid has been achieved. The enzyme was detected in a particulate fraction. Kinetics of the reaction have been studied and the substrate specificity is discussed. Both endogenous colominic acid, bound to the enzyme fraction, and purified, soluble exogenous colominic acid acted as N-AN acceptors, the endogenous acceptor being much more effective. The presence of 1.2 m ammonium sulfate yielded a 4-fold increase of N-AN incorporation into the endogenous colominic acid, and was required for N-AN incorporation into the soluble exogenous colominic acid. The available data suggest that chain elongation proceeds at the nonreducing termini of the polymer, comparable to the formation of glycogen, rather than at the reducing end, as in the case of the bacterial lipopolysaccharides.
Security in wireless mobile and sensor networks

Security plays a significant role in the current and future wireless mobile networks. The goal of secured communication must ensure that the data we receive is authentic, confidential and have not been altered. Because of the characteristics of wireless medium, limited protection of mobile nodes, nature of connectivity and lack of centralized managing point, wireless mobile networks are too vulnerable and often subject to attacks. In this chapter we discuss security issues and challenges in wireless mobile ad hoc and sensor networks as well as in pervasive computing infrastructures. We also describe security protocols for such environments.
ConferenceXP and Advanced Collaborative Scenarios

ConferenceXP is an initiative of Microsoft Research exploring how to make wireless classrooms, advanced realtime collaboration, and distance learning a compelling, rich experience by assuming the availability of emerging and enabling technologies, such as high-bandwidth networks, multicast, wireless devices and Tablet PCs. The ConferenceXP research platform enables researchers to create distributed applications that take advantage of ConferenceXP technology as well as Tablet PCs and wireless networks while enabling them to develop the collaborative tools and applications they need without having to build them from the ground up. By partnering with research organizations and universities, the ConferenceXP project combines the academic communitys expertise in the learning sciences with Microsofts expertise in technology.
Neuromuscular organization in the swimming system of the pteropod mollusc Clione limacina

Swim motor neurons of the pteropod mollusc Clione limacina were identified by a combination of electrophysiological and morphological characteristics. Two types of motor neurons were found, including small motor neurons which are active during both slow and fast swimming and which innervated restricted fields of the ipsilateral wing. General excitor motor neurons have large cell bodies, innervate widespread fields and are recruited into activity for fast swimming. Small motor neurons monosynaptically innervate slow-twitch muscle cells, whereas general excitors monosynaptically innervate both slow-twitch and fast-twitch muscle cells. Activity in general excitors can centrally enhance that in small motor neurons because the neurons are electrically coupled. Neuromuscular recordings and lesion experiments indicate that a peripheral nerve network does not appear to play an important role in the spread of excitation throughout the muscle fields.
The Subjective Beliefs Underlying Probability Overestimation

Teigen (1974a, 1974b, 1983) observed that the numerical probabilities assigned to a set of exhaustive and mutually exclusive events frequently exceed one. Three experiments were performed to examine why these inflated numerical probability judgments form and what they reflect about people's subjective beliefs. Some work suggests that numerical probability overestimations stem from a fundamental misunderstanding of the rules of probability calculation. Our findings, though, indicate that biased hypothesis testing processes operate that contribute to the subjective overestimation of the likelihood of a hypothetical event. People tend to perceive events to be more plausible than is possible because of confirmatory processes characterizing the selective testing of a hypothesis. Our findings indicate that these processes may lead to the unwarranteddisconfirmationof a focal hypothesis when the evidence for all of the alternatives is weak.
Phenotype-based treatment of dietary obesity: differential effects of fenofibrate in obesity-prone and obesity-resistant rats☆

High-fat diets (HFDs) promote hyperphagia and adiposity in animals and human beings. To test the hypothesis that limitations on fat oxidation underlie this propensity for diet-induced obesity, rats were treated with fenofibrate, which enhances fat oxidation mainly in liver by inducing expression of enzymes and proliferation of organelles involved in fatty acid oxidation. Male Sprague-Dawley rats were fed a HFD (42% fat calorie) for 2 weeks. Rats ranked in the top and bottom thirds for weight gain during this feeding period were designated as obesity prone (OP) and obesity resistant (OR), respectively. Fenofibrate was added to the HFD (0.025% wt/wt) for half of the OP and OR rats. During the next 10 days, fenofibrate treatment significantly (P < .05) reduced food intake, weight gain, feed efficiency, and adiposity in OP rats to levels seen in control OR rats, but had no such effects in OR rats. Fenofibrate treatment increased whole-body fatty acid oxidation, and in liver, the expression of carnitine palmitoyl transferase I only in OP rats, but enhanced expression of acyl-CoA oxidase in both OP and OR rats. Restricting food intake of OP rats to levels seen in rats given fenofibrate similarly reduced weight gain but had little effect on weight of fat pads. Treatment with the daily dosage of fenofibrate given as a bolus did not produce a conditioned flavor aversion. These results suggest that enhancement of mitochondrial fatty acid oxidation in liver may be an effective phenotype-based treatment strategy for dietary obesity.
Energy Efficiency Impact of Localized Cooling/Heating for Electric Vehicle

The present paper reports on a study of the HVAC energy usage for an EREV (extended range electric vehicle) implementation of a localized cooling/heating system. Components in the localized system use thermoelectric (TE) devices to target the occupant's chest, face, lap and foot areas. A novel contact TE seat was integrated into the system. Human subject comfort rides and a thermal manikin in the tunnel were used to establish equivalent comfort for the baseline and localized system. The tunnel test results indicate that, with the localized system, HVAC energy savings of 37% are achieved for cooling conditions (ambient conditions greater than 10 °C) and 38% for heating conditions (ambient conditions less than 10 °C), respectively based on an annualized ambient and vehicle occupancy weighted method. The driving range extension for an electric vehicle was also estimated based on the HVAC energy saving.
Formation of silicon carbide in silicon substrates during CF4/H2 dry etching

Abstract Silicon specimens which had been reactive ion etched in CF 4 / X %H 2 (0≤ X ≤40) and subsequently air exposed have been characterised by X-ray photoelectron emission spectroscopy. Angular rotation was used to study films deposited by the plasma process onto the Si surface. In agreement with previous studies it is found that plasma exposure of Si specimens leads to the deposition of a fluorocarbon film. An intriguing new finding was the discovery of subsurface silicon carbide. The existence of this carbide layer was found to be independent of gas composition from 0–40% H 2 for a one-minute plasma exposure. Helium ion channeling studies of the same specimens show Si near-surface disorder. A silicon-carbide formation mechanism is suggested according to which carbon is deposited below the Si surface by the bombardment of carbon containing ions, thus enabling silicon-carbon bonding.
A Million Decisions Life on the (Sustainable Business) Frontier

Innovation often happens at the margin. For the past 5 years, in the academic equivalent of an ecotone, Aquinas College in Grand Rapids, Michigan has built and continues to refine offerings in its 4-year Bachelor of Science degree in Sustainable Business. Emerging out of the demands of a rapidly changing business world and the sustainable business movement, this degree program integrates and spans across disciplines. As the country's first undergraduate program of its kind, Aquinas' program-building effort for its signature Sustainable Business degree offers lessons and insights for those who might embark on a similar journey on the “sustainability frontier.” Faculty creativity, administrative leadership, and external support all contribute to this innovative curriculum.
Personalized Feedback to Improve CPAP Adherence in Obstructive Sleep Apnea

Obstructive sleep apnea (OSA) is effectively treated with continuous positive airway pressure (CPAP). Low rates of CPAP adherence led to the development of a personalized feedback intervention requiring minimal provider burden. In a comparison of the intervention to standard information, group differences failed to reach significance. Explanations for the findings include low power, that machines were not provided, and an atypical sample. Effect sizes were medium to large at 2 weeks, suggesting that sufficiently powered studies may be warranted.
The assessment of platelet function

SUMMARY Platelet activation is involved in physiological hemostasis and in a variety of thromboembolic events leading to stroke, myocardial ischemia, and other organ dysfunction. Apart from congenital platelet dysfunction, acquired platelet defects are increasingly common in patients due to the widespread use of antiplatelet agents. Newer antiplatelet agents targeting platelet glycoprotein IIb–IIIa and adenosine-5′-diphosphate receptors inhibit platelet activation, and therefore assessing platelet inhibition may be important to prevent major bleeding, especially before a surgical intervention. In the past decade, the knowledge from genotypic analyses and prospective outcome studies suggested inter-patient variability in the therapeutic response to antiplatelet therapies, which further stresses the need for individual platelet testing. In managing bleeding patients, platelet transfusion may be better guided by the use of platelet function tests because transfusion therapy is costly and potentially harmful if administered inappropriately. Basic understanding of the hemostatic roles of platelets, etiologies of platelet defects, and characteristics of current platelet assessment methods should help physicians who manage complex coagulation issues in critically ill patients.
The Proto-oncogene Crk-II Enhances Apoptosis by a Ras-Dependent, Raf-1/MAP Kinase-Independent Pathway☆

Abstract Human embryonic kidney 293 cells and 293 cells overexpressing different amounts of the adaptor protein Crk-II (ranging from 3- to 10-fold higher levels than the parental cell line) were examined for their ability to undergo apoptosis when maintained in control and serum-free (SF) medium. Parental 293 cells undergo apoptosis only when deprived of serum for prolonged periods of time (24–48 h). On the other hand, 293 cells overexpressing different levels of Crk-II present detectable levels of apoptosis as measured by DNA fragmentation when grown in control medium, with a marked increase when they are deprived of serum for 12–48 h. To determine the pathways involved in Crk-II-induced apoptosis, Crk-II overexpressing cells were transiently transfected with a dominant-negative Ras construct (N17-Ras). Compared to cells transfected with control vectors, the cells overexpressing N17-Ras presented lower levels of apoptosis when maintained in SF-medium. On the other hand, transient transfection of a dominant-negative Raf-1 construct (K375W-Raf-1) did not decrease apoptosis; slightly increasing DNA fragmentation levels were seen. Similar results were obtained when the cells were incubated in the presence of a MEK1 inhibitor. The results presented here suggest that overexpression of Crk-II induces apoptosis via a Ras-dependent, Raf-1/MEK1/ERK-independent pathway.
Semantic framework for DSLs

Domain-Specific Languages (DSLs) enable domain experts to participate in software development tasks and to specify their own programs using domain abstractions. To define programs using domain concepts, rather than programming language concepts, model-based syntax and semantic specification techniques may offer advantages over current approaches. The purpose of the research described in this paper is to provide a semantic framework that can be used visually by DSL designers, yet has formal underpinnings such that interoperation with verification tools is possible to realize model checking tasks. This research is focused on a visual technique based on activity diagrams and graph transformation rules to define the semantics of DSLs.
Comparative hemopoietic and growth factor responses to vitamin B12, folic acid, and iron

Experimental data have been presented on the effectiveness of vitamin B12, folic acid, and iron on anemia in chicks produced by a basal deficient diet. Hemopoietic and growth factor values for combinations of folic acid, vitamin B12, and iron have been demonstrated in varying dosages and modes of administration. Results illustrate the rate of recovery, growth, and effectiveness of the supplements.
Some comments on the experimental measurement of utility

Experiments designed to measure people's utility functions usually involve choices to be made by subjects among different wagers. As a rule, complex statistical methods are used to decide whether a pattern of choices is consistent with a particular utility function and an associated stochastic decision model. Here the author takes issue with the methods used by two investigators to interpret the results of their experiments.
Effect of Annual Amendments of Compost on Nitrate Leaching in Nursery Stock

Municipal solid waste (MSW) compost was applied at rates of 56 and 112 t/ha (incorporated) and 224 t/ha (mulch) to mitigate topsoil loss in nursery stock production. In two years, nitrate concentrations in ground water beneath all plots remained below 10 ppm with no significant differences between treatments.In another experiment, nitrate in ground water was measured beneath a high coductive sandy terrace soil amended with a variety of composts. In one experiment, spent mushroom compost (SMC) and chicken manure compost (CMC) were applied yearly at rates of 56 and 112 t/ha to provide all the fertilizer requirements for intensive vegetable production. Nitrate concentrations in ground water beneath all compost-amended plots remained below 10 ppm during the three-year study, while concentrations beneath the fertilized control reached 14.7 ppm in an unusually wet spring. After heavy rains, control plots were more susceptible to nitrate leaching than compost-amended plots in the first two years of the study. Th...
BNaC1 and BNaC2 constitute a new family of human neuronal sodium channels related to degenerins and epithelial sodium channels

The recently defined DEG/ENaC superfamily of sodium channels includes subunits of the amiloride-sensitive epithelial sodium channel (ENaC) of vertebrate colon, lung, kidney, and tongue, a molluscan FMRFamide-gated channel (FaNaC), and the nematode degenerins, which are suspected mechanosensory channels. We have identified two new members of this superfamily (BNaC1 and BNaC2) in a human brain cDNA library. Phylogenetic analysis indicates they are equally divergent from all other members of the DEG/ENaC superfamily and form a new branch or family. Human BNaC1 maps to 17q11.2-12 and hBNaC2 maps to 12q12. Northern blot and mouse brain in situ hybridizations indicate that both genes are coexpressed in most if not all brain neurons, although their patterns of expression vary slightly, and are expressed early in embryogenesis and throughout life. By analogy to the ENaCs and the degenerins, which form heteromultimeric channels, BNaC1 and BNaC2 may be subunits of the same channel.
Acute toxicity of CD40 stimulation following syngeneic bone marrow transplantation

Abstract CD40 stimulation, by either antibody or ligand has been demonstrated to selectively inhibit the growth of various neoplastic cells in vitro and in vivo. We first assessed the effects of CD40 stimulation on normal mice using both a recombinant soluble ligand (srCD40L) or an agonist mAb, and found that B cell expansion occurred but no overt toxicity was observed. Surprisingly, when CD40 stimulation was administered following a syngeneic bone marrow transplant (BMT), all mice receiving as little as 10 ug injections of anti-CD40 antibody succumbed within 4 days whereas mice receiving the srCD40L did not show any adverse effects. Histological evaluation of the mice indicated that mice treated with CD40 mAbs exhibited significant gut pathology with marked crypt hyperplasia, goblet cell depletion, and villous blunting in the gut. Delaying administration of the anti-CD40 mAb resulted in protection from this toxicity. As CD40 stimulation has been shown to induce cytokine production by monocytes and other CD40+ cells, we hypothesized that cytokines may be responsible for mediating the pathology following BMT. Serum cytokine levels of mice following the BMT revealed that mice receiving antibodies to CD40 had markedly elevated levels of interferon-gamma. Interestingly, mice receiving the srCD40L had no increases in interferon levels indicating that interferon levels correlated with pathology. Interferon-gamma knockout (KO) mice were then used as recipients of syngeneic BMT with or without anti-CD40 treatment. Treatment of these KO mice with anti-CD40 resulted in significantly greater increases in survival compared to control mice receiving the antibodies. These results indicate that CD40 stimulation using agonist antibodies following BMT can induce a fatal cytokine-induced disease affecting the gut tissues.
Singlet oxygen reactivity of bilirubin and related tetrapyrroles

The rates of chemical reactivity (kR) and physical quenching (kQ) of singlet oxygen by bilirubin IXα, mesobilirubin IXα, bilirubin IXα dimethyl ester, aetiobilirubin IVγ, biliverdin IXα, biliverdin IXα dimethyl ester, aetiobiliverdin IVγ and an oxodipyrromethene have been determined. The kR and kQ values approach the diffusion threshold for the bilirubin-like substrates, but kR<kQ by about a factor of 103 for the verdins. A reaction mechanism involving superoxide ion is suggested. Bilirubin appears to quench singlet oxygen by an electron-transfer mechanism.
Efficient Exciton Quenching by Hole Polarons in the Conjugated Polymer MEH‐PPV

Recently published near field scanning optical measurements (NSOM) on the conjugated polymer MEH-PPV exhibited a strong dependence of the photoluminescence intensity on the applied electric fields at the NSOM tip. The observed effect is apparently due to exciton quenching by hole polarons. In the present paper, a model "single carrier" electro-modulated-photoluminescence device is used to further explore the exciton quenching effect of hole polarons in MEH-PPV. Hole polarons, created by charge injection from an ITO electrode, are observed to dramatically quench the photoluminescence intensity of MEH-PPV. The Stern-Volmer quenching efficiency of a hole polaron in conjugated polymer thin films was measured to be 390 nm 3 . This value, and other data presented herein, are consistent with the published NSOM photoluminescence modulation measurements and offer further evidence that hole polarons are efficient photoluminescence quenchers in MEH-PPV.
Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called “length bias”, will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology categories that include longer genes are more likely to be identified as enriched. These categories, however, are not necessarily biologically more relevant. We show that one can effectively adjust for length bias in Gene Ontology analysis by including transcript length as a covariate in a logistic regression model. The logistic regression model makes the statistical issue underlying length bias more transparent: transcript length becomes a confounding factor when it correlates with both the Gene Ontology membership and the significance of the differential expression test. The inclusion of the transcript length as a covariate allows one to investigate the direct correlation between the Gene Ontology membership and the significance of testing differential expression, conditional on the transcript length. We present both real and simulated data examples to show that the logistic regression approach is simple, effective, and flexible.
Design of school bus routes by computer

Abstract A practical method for generating school bus routes and schedules on a digital computer has been developed. Routing is accomplished by a two step procedure. First, the shortest route a bus of infinite capacity traverses in order to visit all of the stops is determined. This route, the solution of the traveling-salesman problem associated with the set of bus stops, is obtained by an efficient heuristic procedure which yields near-optimal solutions to problems of a realistic size. This single route is then partitioned to provide individual bus routes and schedules which satisfy bus capacity, bus loading policy, and passenger riding time constraints.
The electrocardiographic manifestations of cyclic antidepressant therapy and overdose: a review.

Abstract Cyclic antidepressants may cause changes in the electrocardiogram at therapeutic or toxic serum levels. The most serious complications of cyclic antidepressant toxicity are dysrhythmas, hypotension, and seizures. It is predominantly the cardiotoadc effects that cause mortality. Once cardiotoxicity is evident, the treatment of choice is serum alkalinization, preferably by sodium bicarbonate therapy. In order to predict which overdose patients are at high risk for complications, electrocardiographic criteria have been identified as reliable screens. For “first generation” tricyclic antidepressants, QRS prolongation (particularly > 100 msec) and a terminal 40-ms frontal plane axis > 120° are the most sensitive. This article reviews antidepressant pharmacology, electrocardiographic manifestations of antidepressant cardiotoxicity, and approaches to treatment of antidepressant-induced conduction disturbances and dysrhythmias.
Staurosporine-derived inhibitors broaden the scope of analog-sensitive kinase technology.

Analog-sensitive (AS) kinase technology is a powerful approach for studying phospho-signaling pathways in diverse organisms and physiological processes. The key feature of this technique is that a kinase-of-interest can be mutated to sensitize it to inhibitor analogs that do not target wild-type (WT) kinases. In theory, this enables specific inhibition of any kinase in cells and in mouse models of human disease. Typically, these inhibitors are identified from a small library of molecules based on the pyrazolopyrimidine (PP) scaffold. However, we recently identified a subset of native human kinases, including the Ephrin A kinase family, that are sensitive to commonly used PP inhibitors. In an effort to develop a bioorthogonal AS-kinase inhibitor and to extend this technique to PP-sensitive kinases, we sought an alternative inhibitor scaffold. Here we report the structure-based design of synthetically tractable, potent, and extremely selective AS-kinase inhibitors based on the natural product staurosporine....
Morphologic and histologic outcomes of tongue reduction surgery in an animal model

Objective To describe the effect of anterior tongue reduction surgery on tongue size, morphology, and histology. Design Prospective experiment. Materials Twenty-two 12-week-old Yucatan minipigs. Methods Six sibling pairs had tongue reduction (Group B) or sham surgery (Group A), and underwent euthanasia the day of surgery. Five sibling pairs had tongue reduction (Group D) or sham surgery (Group C), and were raised for four weeks. Data collected included changes in tongue morphology, histology, and animal response to surgery. Results All animals tolerated surgery and maintained their weight. Tongue size was uniformly reduced in all animals as compared to sham surgery. Tongue reduction was stable long term in Group D. All animals had normal wound healing and neurovascular structure preservation. Fibrosis occurred at the repair site. Conclusion Midline tongue reduction resulted in uniform tongue reduction in all dimensions and volume, without damaging neurovascular structures. Localized fibrosis is a sequela of healing.
Revascularization and ventricular restoration in patients with ischemic heart failure: the STICH trial.

Purpose of review As techniques for the management of patients with ischemic heart failure have evolved, controversy has arisen with respect to the roles of revascularization and ventricular restoration procedures. This review addresses current thinking on the management of these patients and describes a prospective randomized trial that will have an impact on future treatment selection. Recent findings Although the basis for improved survival with coronary artery bypass grafting lies in the viability of ischemic myocardium, nuclear medicine studies and stress echocardiography have failed to adequately select for tissues that are capable of recovery. Recent studies have suggested an additional benefit to combining ventricular restoration with bypass surgery. However, the role for these techniques has not been definitively established. Summary The currently enrolling Surgical Treatment for Ischemic Heart Failure (STICH) trial promises to address these issues and thereby improve the management of patients with this disease.
Exchange between Long Island Sound and adjacent waters

[1] We exploit archived salinity data, averaged by month for the years 1995–2001, to evaluate exchange of salt between Long Island Sound and shelf waters, and treat Long Island Sound as a control volume with eastern and western boundaries at The Race and the East River, respectively. The use of inverse methods to solve a system of equations expressing conservation of salt and water provides estimates of model parameters together with uncertainty estimates and measures of model performance. We explore the use of a single exchange coefficient acting on an axial salinity gradient to represent exchange at The Race and find that it is necessary to allow the coefficient to depend weakly on variability of freshwater discharge, R, into the sound, i.e., = ()0.2(1,600 ± 200) m2/s. Using established estimates of the mean circulation at the western boundary of the sound, we determine a dispersion coefficient in the Upper East River of 300 ± 200 m2/s. Explicitly modeling the advective exchange flow (gravitational circulation) at The Race using a coefficient that varies as the one-third power of the normalized discharge indicates that gravitational circulation accounts for less than 10% of the up-estuary salt flux in eastern Long Island Sound.
Debugging optimized code without being misled

Correct optimization can change the behavior of an incorrect program; therefore at times it is necessary to debug optimized code. However, optimizing compilers produce code that impedes source-level debugging.Optimization can cause an inconsistency between where the user expects a breakpoint to be located and the breakpoint's actual location. This article describes a mapping between statements and breakpoint locations that ameliorates this problem. The mapping enables debugger behavior on optimized code that approximates debugger behavior on unoptimized code sufficiently closely for the user to use traditional debugging strategies.Optimization can also cause the value of a variable to be noncurrent—to differ from the value that would be predicted by a close reading of the source code. This article presents a method of determining when this has occurred, and shows how a debugger can describe the relevant effects of optimization. The determination method is more general than previously published methods; it handles global optimization and many flow graph transformations, and it is not tightly coupled to optimizations performed by a particular compiler. Necessary compiler support is also described.
Climate Change Position Statement, Dissenting View

I served on the AGU panel to draft the updated position statement on climate change. We were charged by AGU to provide “an up-to-date statement [that] will assure that AGU members, the public, and policy makers have a more current point of reference for discussion of climate change science that is intrinsically relevant to national and international policy.”
Predicting Discharge Disposition Among Adolescents in Residential Treatment

ABSTRACT The major goal of this study was to identify early risk factors for unsuccessful discharges among a sample of boys aged 12 to 17 in residential treatment. Three of the risk factors considered independently predicted unsuccessful discharge. Legal status at admission (person in need of supervision or juvenile delinquent), being older at admission, and exhibiting very serious emotional and behavioral problems during the first two months at the residential treatment center each were associated with increased likelihood of unsuccessful discharge. A secondary goal of the study was to describe and predict the types of emotional and behavioral problems boys exhibited during the transition (first two months) into residential treatment, as indicated by ratings of case records for a modified simple random sample of these youth. “Very serious” problems were exhibited by one-third of the boys. However, neither age nor legal status at admission, only prior psychiatric hospitalization, predicted occurrence of “...
Atmospheric rivers induced heavy precipitation and flooding in the western U.S. simulated by the WRF regional climate model

[1] A 20-year regional climate simulated by the Weather Research and Forecasting model has been analyzed to study the influence of the atmospheric rivers and land surface conditions on heavy precipitation and flooding in the western U.S. The simulation realistically captured the mean and extreme precipitation, and the precipitation/temperature anomalies of all the atmospheric river events between 1980–1999. Contrasting the 1986 President Day and 1997 New Year Day events, differences in atmospheric stability have an influence on the spatial distribution of precipitation. Although both cases yielded similar precipitation, the 1997 case produced more runoff. Antecedent soil moisture, rainfall versus snowfall, and existing snowpack all seem to play a role, leading to a higher runoff to precipitation ratio for the 1997 case. This study underscores the importance of the atmospheric rivers and land surface conditions for predicting heavy precipitation and floods in the current and future climate of the western U.S.
Histamine affects STAT6 phosphorylation via its effects on IL-4 secretion: role of H1 receptors in the regulation of IL-4 production.

Abstract Signal Transducer and Activator of Transcription (STAT)-6 is a transcriptional factor activated mainly through the cytokines IL-4 and IL-13 leading to the Th2 cell differentiation. Th2 cells play a role in the etiology and pathogenesis of allergic disease. Histamine alters the Th1/Th2 cytokine balance towards the Th2 cytokine profile and consequently plays a role in allergic diseases and asthma. This study was designed to investigate the effects of histamine on the STAT6 phosphorylation. C57/BL6 splenocytes were pretreated with different concentrations of histamine (10− 4 M to 10− 13 M) followed by stimulation with PMA+ionomycin or IL-4. The phosphorylated and total basal STAT6 levels were assessed by employing the immunoblotting technique. Histamine caused the hyper-phosphorylation of STAT6. H1 receptor antagonist pyrilamine reversed the effect of histamine on STAT6 phosphorylation. However, H2 receptor antagonist ranitidine and H3/H4 receptor antagonist thioperamide did not affect the histamine mediated hyper-phosphorylation of STAT6. Furthermore, H1 receptor agonist betahistine enhanced the phosphorylation of STAT6 whereas H2 receptor agonist amthamine did not affect the phosphorylation STAT6. Furthermore, tyrosine kinase inhibitor, tyrphostin, inhibited the histamine mediated phosphorylation of STAT6 when stimulated with PMA + ionomycin. The effects of histamine on the STAT6 phosphorylation were indirect since they were blocked either by the antibodies to IL-4 and IL-13 or in IL-4 knock out mice in the presence of IL-13 antibody. These observations suggest that histamine indirectly affected the STAT6 phosphorylation via its effects on the secretion of cytokines (IL-4) and H1 receptor played a role in this process.
The differential synthesis and degradation of ribosomal DNA during the vegetative cell cycle in Chlamydomonas reinhardi.

A model is proposed relating rDNA metabolism in Chlamydomonas with nucleolar breakdown and formation during a single cell cycle.
Proability estimation usind a multinominal logistic function

A multinomial logistic model is used for estimating the probabilities of k mutually exclusive and exhaustive events as a function of p independent variables. The parameters are estimated by maximum likelihood involving non-linear iterative techniques. Careful attention is given to the computational procedure which involves the estimation of (k − 1) (p + 1) parameters. The prediction of the probability of respiratory distress syndrome (RDS) in human newborns is presented as an example, It was found that initial estimates obtained from the linear discriminant functions often were far from the maximum likelihood solution and that simple Newton-Raphson procedures often diverge. The final algorithm has been tested on many data sets and has always converged.
New approaches to disease mapping in admixed populations

Admixed populations such as African Americans and Hispanic Americans are often medically underserved and bear a disproportionately high burden of disease. Owing to the diversity of their genomes, these populations have both advantages and disadvantages for genetic studies of complex phenotypes. Advances in statistical methodologies that can infer genetic contributions from ancestral populations may yield new insights into the aetiology of disease and may contribute to the applicability of genomic medicine to these admixed population groups.
Engagement study of an integrated rehabilitation robotic tablet-based gaming system

Physical therapy is a common treatment for the rehabilitation of hemiparesis, or the weakness of one side of the body. However, a significant issue in the therapy process is that patients may struggle with motivation to complete the required therapy sessions. For this purpose, a rehabilitation gaming system was created that combines a hand rehabilitation robot with a gaming application on a tablet to promote engagement and discourage boredom. A study was also conducted to compare engagement between the gaming system and traditional therapeutic exercises. The results of this study show that participants prefer playing rehabilitation games more than they do exercising with traditional rehabilitation methods. On average, participants spent approximately four times longer playing the rehabilitation game before becoming bored than they did with traditional exercises. From their responses to the retrospective survey, the participants experienced significantly more enjoyment and engagement when exercising with the tablet game. They also experienced significantly less boredom. The participants unanimously agreed that if they were required to exercise their wrists for an hour a day, as is a normal requirement for patients in stroke therapy, that they would prefer to do so by playing the tablet game.
Critical Duration in Visual Brightness Discrimination for Retinal Areas of Various Sizes

In this study visual brightness discrimination was investigated for three centrally fixated incremental areas (1° 20′, 5°, and 19°) each superimposed upon a 26° surround. Surround luminances from logI=3.48 to logI=−3.02 (millilamberts) were used. The objectives of the experiment were to find: (a) the shape of the transition between the two theoretical conditions It=constant and I=constant as the duration of incremental exposure was increased, and (b) the magnitudes of the critical durations at which this transition occurred.The results indicated that the transition between conditions It=constant and I=constant for central fixation was relatively sharp, regardless of field size or luminance level. This was true for both differential and absolute threshold determinations. The critical durations, depending upon field size, ranged from 0.02–0.06 second at high luminances to as long as 0.20–0.35 second at low scotopic luminance levels. The curves relating critical duration to log luminance showed irregularities in the mesopic range for the two larger fields. These irregularities were interpreted as indicating a possible transition between rod and cone functioning in this luminance range.
Synthesis of Optically Active α-Amino Esters via Dynamic Kinetic Resolution: A Mechanistic Study

Synthesis of N-protected optically active α-amino esters from racemic α-halo esters via dynamic kinetic resolution (DKR) will be described. This methodology is general in nature and provides the desired optically active N-protected amino esters in 70−95% yield with diastereomeric excesses in the range of 85 to >98%. Applications and mechanistic aspects will be discussed.