cssi/SciSciGPT-SciSciNet huggingface dataset:
Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction

Protein-peptide interactions play an important role in many cellular processes. In silico prediction of protein-peptide complex structure is highly desirable for mechanistic investigation of these processes and for therapeutic design. However, predicting all-atom structures of protein-peptide complexes without any knowledge about the peptide binding site and the bound peptide conformation remains a big challenge. Here, we present a docking-based method for predicting protein-peptide complex structures, referred to as MDockPeP, which starts with the peptide sequence and globally docks the all-atom, flexible peptide onto the protein structure. MDockPeP was tested on the peptiDB benchmarking database using both bound and unbound protein structures. The results show that MDockPeP successfully generated near-native peptide binding modes in 95.0% of the bound docking cases and in 92.2% of the unbound docking cases. The performance is significantly better than other existing docking methods. MDockPeP is computationally efficient and suitable for large-scale applications.
Individual clotting factor contributions to mortality following trauma.

BACKGROUND Acute traumatic coagulopathy affects 20% to 30% of trauma patients, but the extensive collinearity of the coagulation cascade complicates attempts to clarify global clotting factor dysfunction. This study aimed to characterize phenotypes of clotting factor dysfunction and their contributions to mortality after major trauma. METHODS This prospective cohort study examines all adult trauma patients of the highest activation level presenting to San Francisco General Hospital between February 2005 and February 2015. Factors II, V, VII, VIII, IX, and X and protein C activity on admission and mortality status at 28 days were assessed. Predictors of 28-day mortality in univariate analysis were included in multiple logistic regression controlling for traumatic brain injury (TBI), acidosis, age, and mechanism of injury. Principal component analysis was utilized to identify phenotypic coagulation. RESULTS Complete coagulation factor data were available for 876 (61%) of 1,429 patients. In multiple logistic regression, factors V (odds ratio [OR], 0.86; 95% confidence interval [CI], 0.76-0.97), VIII (OR, 0.97; 95% CI, 0.95-0.99), and X (OR, 0.79; 95% CI, 0.68-0.92) and protein C (OR, 1.17; 95% CI, 1.05-1.30) significantly predicted 28-day mortality after controlling for age, base deficit, mechanism of injury, and TBI. Principal component analysis identified two significant principal components (Phenotypes 1 and 2) that accounted for 66.3% of the total variance. Phenotype 1 (factors II, VII, IX, and X and protein C abnormalities) explained 49.3% and was associated with increased injury, coagulopathy, TBI, and mortality. Phenotype 2 (factors V and VIII abnormalities) explained 17.0% and was associated with increased coagulopathy, blunt injury, and mortality. Only Phenotype 2 remained significantly associated with 28-day mortality in multiple logistic regression. CONCLUSIONS Principal component analysis identified two distinct phenotypes within the entirety of global clotting factor abnormalities, and these findings substantiate the crucial association of factors V and VIII on mortality following trauma. This may be the first step toward identifying unique phenotypes after injury and personalizing hemostatic resuscitation. LEVEL OF EVIDENCE Prognostic study, level III.
Effects of environment and structural stability on the low cycle fatigue behaviour of nickel-base superalloys

The effects of microstructural stability and environmental degradation on the low cycle fatigue life of nickel-base superalloys at elevated temperature are considered. Alloys such as Rene 80 and Re...
Whole body control of a wheeled inverted pendulum humanoid

We present a method to implement operational space control technique for whole body control of a wheeled-inverted pendulum (WIP) humanoid, a class of robots that feature a redundant manipulator dynamically balancing itself on two wheels. We consider the case in which the base link is not passive, in that, the reaction of the torque driving the wheels is acting on the base link. This makes the system underactuated because the number of actuators is less than the degrees of freedom. However, it is a special form of underactuation where all degrees of freedom are actuated, with one actuator being shared by two degrees of freedom. This special feature of WIP dynamics challenges the straightforward application of operational space techniques, compared to fully actuated, constrained, or underactuated systems with no DOFs sharing the actuators. The key idea is to isolate dynamics of the manipulator from the wheel dynamics and to control the resulting system using operational-space control. A side-effect of this is the resulting asymmetry of the inertia matrix restricting full use of operational space tools. This is addressed by presenting a coordinate transformation that transforms the inertia matrix into a symmetric one. Finally, the wheel dynamics is derived as a function of manipulator joint accelerations so that horizontal motion of the robot can be treated as another task being controlled within the framework developed for manipulator control. Simulation results are presented on a five degree of freedom planar robot, with four DOF serial arm mounted on wheels.
Determination of Glycoalkaloids in Potatoes and Potato Products by Microwave Assisted Extraction

Potato glycoalkaloids can reach levels that are harmful to human health. A rapid and reliable microwave assisted extraction method for quantitative analysis of α-solanine and α-chaconine content in raw potato and potato based products is presented. A chemical microwave was used to determine optimal temperature and pressure conditions for the extraction of α-solanine and α-chaconine from Idaho grown tubers and six commercially available mashed potato products. Recovery efficiency of glycoalkaloids was 37% greater by microwave assisted extraction (19.92 mg/kg glycoalkaloid) as compared to conventional solid/liquid methods (12.51 mg/kg glycoalkaloid). Optimal extraction of glycoalkaloids from potato samples dissolved in methanol was achieved using a microwave reactor set to 90 °C for ten minutes. The interior of Idaho grown tubers was determined to contain lower levels of glycoalkaloids (19.92 mg/kg dry weight; 6.5 ± 1.78 mg α-solanine and 13.40 ± 1.65 mg α-chaconine), as compared to commercial potato products (33.86–81.59 mg/kg).
Predicting the mental health outcomes for Ebola first responders

Purpose: The 2014 Ebola epidemic resulted in 26,683 cases and 11,022 deaths by May 6th, 2015. With first responders deploying from the United States to assist with the many challenges being faced in the field, they encountered a new set of traumatic events and situations that undoubtedly put them at risk for developing a mental disorder. Organizations must be prepared to provide mental health services for their employees and volunteers once they return. Approach: The authors questioned the potential prevalence of PTSD, ASD, and depression among returning first responders and which therapy method would be the most effective in terms of an individual’s recovered or improved condition. This was done through the use of AnyLogic® 7.0. An agent-based method to model the stress levels a first responder may experience while dealing with Ebola was used, where all responders begin in the healthy state and can develop mental health disorders. The therapy options tested were Cognitive Processing Therapy, Prolonged Exposure, and Group Based Exposure Therapy. Results: GBET for PTSD patients provided the most positive results in terms of condition recovery and improvement. Conclusion: The results showed evidence that the type of therapy used can drastically affect the individual’s mental health outcome.
Diagnosis and Management of Heart Failure in Older Adults

Aging is characterized by heterogeneity, both in health and illness. Older adults with heart failure often have preserved ejection fraction and atypical and delayed clinical manifestations. After diagnosis of heart failure is established, a cause should be sought. The patient's comorbidities may provide clues. An elevated jugular venous pressure is the most reliable clinical sign of fluid volume overload and should be carefully evaluated. Left ventricular ejection fraction must be determined to assess prognosis and guide therapy. These 5 steps, namely, diagnosis, etiologic factor, fluid volume, ejection fraction, and therapy for heart failure may be memorized by mnemonic: DEFEAT-HF.
Lexical and Syntactic Features Selection for an Adaptive Reading Recommendation System Based on Text Complexity

The goal of this work is to build a classifier that can identify text complexity in service of English as a Second Language (ESL) learners. In order to present language learners with texts that are suitable to their level of English, a set of features that can best describe the lexical and syntactic complexity of a given text were identified. Using a corpus of 355 texts which had already been classified into three different levels of difficulty, I built two different models with different sets of features. These models were tested using four popular machine learning algorithms. The recall of the SVM classifier, who achieved the best results, is 0.87 and its precision is 0.88.
Religious Affiliation, Religiosity, and Spirituality in Pediatric Residents: Effects on Communication and Self-Efficacy with Adolescents in a Clinical Setting

Religion and spirituality are known influences on medical providers' care of patients, but no studies have assessed resident beliefs related to patient perception of clinical care. The main objective of our study was to assess resident religious affiliation, religiosity, and spirituality in relation to self-efficacy and communication with patients during adolescent clinic visits. We found that religious affiliation and religiosity appear to affect patient perception of communication with residents during adolescent visits; spirituality had little noted effect. Further research is warranted, especially regarding resident and patient gender correlations and differences in religious affiliation effects on patient perception of care.
Nup62-mediated nuclear import of p63 in squamous cell carcinoma

Nuclear pore complexes (NPCs) are multiprotein channels that bridge the nucleus with the cytoplasm and regulate all nucleo‐cytoplasmic traffic. NPCs are built by the repetition of ~30 different proteins known as nucleoporins (Nups). Accumulating evidence has revealed a diversity in NPC composition that is critical for cell‐specific functionality and fate determination. A new report by Hazawa et al [1] now identifies the central transport channel nucleoporin Nup62 as a novel regulator of cell proliferation and differentiation in squamous cell carcinoma (SCC), via modulation of p63 nucleo‐cytoplasmic transport. These findings provide further evidence on how alterations in NPC composition might be utilized to determine cell fate.
MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat

HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate the binding interactions of the maturation inhibitor bevirimat (BVM) using very thin frozen-hydrated, 3D microcrystals of a CTD-SP1 Gag construct with and without bound BVM. The 2.9-A MicroED structure revealed that a single BVM molecule stabilizes the six-helix bundle via both electrostatic interactions with the dimethylsuccinyl moiety and hydrophobic interactions with the pentacyclic triterpenoid ring. These results provide insight into the mechanism of action of BVM and related maturation inhibitors that will inform further drug discovery efforts. This study also demonstrates the capabilities of MicroED for structure-based drug design.
Latent homomorphism and content satisfaction: The double life of Turkic auxiliary -(I)p bol-

This paper argues that the Turkic auxiliary construction –(I)p bol–, at least in Uyghur and Uzbek, is actually a pair of auxiliaries with distinct meanings. The first auxiliary is described as expressing “full completion” of the event, but its use is highly restricted, to events with incremental or universally quantified themes. Using targeted context-based elicitation, we find that the expression of completion is indirect. Instead, the auxiliary asserts that the event description is homomorphic, in that all of its events are both event-mapped and theme-mapped. Homomorphism requires every part of the theme to undergo a part of the event, and this derives the reported sense of completion. The second auxiliary is not attested in the literature. It applies to all kinds of events, and expresses what we call “content satisfaction,” the conventional implicature that the event as described satisfies some salient propositional content by rendering it true. For instance, it makes part of a plan come to fruition. This plan is presupposed, and the content is accessible through a content-generating function. We apply the methodologies of formal semantic fieldwork to tease these auxiliaries apart, including scope tests that apply differently to the two auxiliaries. Having distinguished them, we suggest new ways to typologically distinguish Turkic auxiliaries and auxiliaries cross-linguistically.
Learning forgiving hash functions: algorithms and large scale tests

The problem of efficiently finding similar items in a large corpus of high-dimensional data points arises in many real-world tasks, such as music, image, and video retrieval. Beyond the scaling difficulties that arise with lookups in large data sets, the complexity in these domains is exacerbated by an imprecise definition of similarity. In this paper, we describe a method to learn a similarity function from only weakly labeled positive examples. Once learned, this similarity function is used as the basis of a hash function to severely constrain the number of points considered for each lookup. Tested on a large real-world audio dataset, only a tiny fraction of the points (∼0.27%) are ever considered for each lookup. To increase efficiency, no comparisons in the original high-dimensional space of points are required. The performance far surpasses, in terms of both efficiency and accuracy, a state-of-the-art Locality-Sensitive-Hashing based technique for the same problem and data set.
Introduction into Diagnostic Clinical Research

An expert clinician needs to take interest in the report on a piece of diagnostic research when its result is of the appropriate form – still very rare – and addresses the full complexity of a diagnostic challenge encountered in his/her particular discipline. When these requirements are satisfied, (s)he needs to determine how this result was produced, and on this basis to be able to evaluate the validity of its empirical content. And if (s)he deems the validity to be adequate, she needs to take interest in the precision of the diagnostic information in the result. For all this, (s)he needs true understanding of the theory of diagnostic research. This constitutes a challenge, notably as fundamental fallacies characterize today’s ‘clinical epidemiology’ in this regard.
Patient-specific predictors of failure to rescue after pancreaticoduodenectomy.

Abstract Background Failure to rescue (FTR) is a recently described outcome metric for quality of care. However, predictors of FTR have not been adequately investigated, particularly after pancreaticoduodenectomy. We aim to identify predictors of FTR after pancreaticoduodenectomy. Methods We reviewed all patients who developed serious morbidity after pancreaticoduodenectomy from 2005 to 2012 in the ACS-NSQIP database. Logistic regression was used to identify preoperative and postoperative risks for 30-day mortality within a development cohort (randomly selected 80%). A score was created using weighted beta coefficients. Predictive accuracy was assessed on the validation cohort (remaining 20%) using a receiver operator characteristic curve and calculating the area under the curve (AUC). Results The FTR rate was 7.2% after pancreaticoduodenectomy (n = 5,027). We identified 5 independent risk factors: age ≥65 and albumin ≤3.5 g/dL, preoperatively; and development of shock, renal failure, and reintubation, postoperatively. The generated score had an AUC = 0.83 (95% CI, 0.77–0.89) in the validation cohort. Using the score: 1*Albumin ≤3.5 g/dL + 2*Age ≥ 65 + 2*Shock + 5*Renal failure + 5*Reintubation, FTR rates increased with increasing score (p Conclusion FTR rates have previously been shown to be associated with hospital factors. We show that FTR is also associated with preoperative and postoperative patient-specific factors.
New York City’s Reuse Impact Calculator: Quantifying the zero waste impact of materials reuse:

In 2015, the city of New York (NYC) introduced a plan to reduce the volume of collected solid waste by 90% by 2030 and envisioned the expansion of reuse opportunities as one of its main drivers. Th...
Splenogonadal fusion: A rare finding during routine orchiopexy

Splenogonadal fusion remains a rare congenital anomaly, with limited reports in the literature. It is important to be aware of this benign condition as orchiectomy can result from confusion with malignant processes. We present a case of splenogonadal fusion in a 12-month-old healthy male with history of cryptorchidism found at the time of surgery.
Machine Learning for Error Correction with Natural Redundancy

The persistent storage of big data requires advanced error correction schemes. The classical approach is to use error correcting codes (ECCs). This work studies an alternative approach, which uses the redundancy inherent in data itself for error correction. This type of redundancy, called Natural Redundancy (NR), is abundant in many types of uncompressed or even compressed files. The complex structures of Natural Redundancy, however, require machine learning techniques. In this paper, we study two fundamental approaches to use Natural Redundancy for error correction. The first approach, called Representation-Oblivious, requires no prior knowledge on how data are represented or compressed in files. It uses deep learning to detect file types accurately, and then mine Natural Redundancy for soft decoding. The second approach, called Representation-Aware, assumes that such knowledge is known and uses it for error correction. Furthermore, both approaches combine the decoding based on NR and ECCs. Both experimental results and analysis show that such an integrated scheme can substantially improve the error correction performance.
Chapter 5 Sperm Guidance into Teleost Fish Egg

Micropyle is a thin canal in the envelope (chorion) of teleost egg. This is the only place in the chorion that permits sperm entry. Spermatozoa swimming freely in water have one- or three-dimensional trajectory. Once in contact with egg’s chorion, spermatozoa initiate thigmotactic (sliding) motion along the chorion surface. Although this “two-dimensional” sperm movement facilitates sperm’s search for the micropyle, there is a specific glycoprotein around the outer opening of the micropyle which directs spermatozoa into the canal. It is called the “micropylar sperm attractant” or MISA. In herring, there is another known factor called the sperm “motility-initiation factor” or SMIF which renders intrinsically motionless spermatozoa motile. For herring, both SMIF and MISA are necessary for sperm entry into the micropyle. The herring micropyle is a thin, manhole-like canal with a slight depression of chorion around the micropyle. This is called Type I micropyle. Other fish with Type I micropyle, with or without a chorionic depression around the micropyle, include flounder, pollack, and munmichog. Some other fish (e.g., salmon, cod, and pufferfish) have a funnel-like micropyle with a wide, conical mouth (Type II). In fish with Type I and II micropyles, except for herring, sperm entry into the micropyle is possible without MISA; however, entry becomes inefficient as most spermatozoa swim over the micropyle. In another group of fish (e.g., goldfish, loach, and zebrafish), the chorion around the micropyle is deeply indented like a large sinkhole or has radially or spirally arranged grooves (Type III micropyle). MISA is absent from the chorion of Type III fish eggs. For fish with Types I and II micropyles, chemical interactions between spermatozoa and chorion around the micropyle assist sperm entry into the micropyle, whereas in those with Type III micropyles, sperm entry is purely physical. In this case, physical configurations of the chorion around the micropyle “directs” spermatozoa toward the micropyle.
Lymphoid Neoplasms with “Benign” Clinical Course or Unclear Malignant Potential

The recently updated WHO classification of tumors of hematopoietic and lymphoid tissue recognized early lesions of lymphoid neoplasm which include monoclonal B-lymphocytosis, in situ mantle cell lymphoma, and in situ follicular neoplasia. These early lesions or indolent lymphomas may have features overlapping with more aggressive lymphoid neoplasms. It is important these entities could be correctly diagnosed to avoid overtreatment.
Survival benefit and phenotypic improvement by hamartin gene therapy in a tuberous sclerosis mouse brain model.

Abstract We examined the potential benefit of gene therapy in a mouse model of tuberous sclerosis complex (TSC) in which there is embryonic loss of Tsc1 (hamartin) in brain neurons. An adeno-associated virus (AAV) vector (serotype rh8) expressing a tagged form of hamartin was injected into the cerebral ventricles of newborn pups with the genotype Tsc1cc (homozygous for a conditional floxed Tsc1 allele) SynI-cre+, in which Tsc1 is lost selectively in neurons starting at embryonic day 12. Vector-treated Tsc1ccSynIcre+ mice showed a marked improvement in survival from a mean of 22 days in non-injected mice to 52 days in AAV hamartin vector-injected mice, with improved weight gain and motor behavior in the latter. Pathologic studies showed normalization of neuron size and a decrease in markers of mTOR activation in treated as compared to untreated mutant littermates. Hence, we show that gene replacement in the brain is an effective therapeutic approach in this mouse model of TSC1. Our strategy for gene therapy has the advantages that therapy can be achieved from a single application, as compared to repeated treatment with drugs, and that AAV vectors have been found to have minimal to no toxicity in clinical trials for other neurologic conditions. Although there are many additional issues to be addressed, our studies support gene therapy as a useful approach in TSC patients.
Impacts of village isolation on childhood nutritional status in rural Malawi

# Background According to a recent 2018 survey, the rate of childhood acute malnutrition in Malawi has decreased while the rate of stunting in children under five has remained at 37.4%. Our study assesses the impact of child sex, child age, and household distance from main road access on nutritional status in rural Malawi. # Methods Anthropometric data was collected on a sample of children aged 0-18 years at three sites in rural Malawi. Z-scores were calculated based on normative height-for-weight and height-for-age World Health Organization (WHO) growth curves. Univariate odds ratios and 95% confidence intervals (CIs) were calculated for the association of the assessed risk factors with stunting prevalence. # Results 198 children were assessed \[46.4% male (92)\]. Children were grouped ages 0- 10 km (52%). Village distance of ≥10 km from the main road (OR = 2.91, CI = 1.26-6.75) and child age under 2 years (odds ratio, OR = 5.54, 95% CI = 1.61-19.1) were both significantly associated with childhood stunting. # Conclusions Within our sample, village distance ≥10 km from the main road and child age <2 years were both significantly associated with stunting. Our results suggest the need for greater resource access and allocation to isolated communities for future public health interventions.
Dental Screening in Elective Total Joint Arthroplasty: Risk Factors for Failure.

Abstract Background Active dental infection at the time of total joint arthroplasty (TJA) or in the acute postoperative period following TJA is thought to increase the risk of periprosthetic joint infection (PJI). Many surgeons recommend preoperative dental screening. This study aimed to identify how many elective TJA patients failed preoperative dental screening and what patient risk factors were associated with failure. Methods A consecutive series of elective, primary TJA was reviewed from 8/1/2016 to 8/1/2017. We studied 511 operations in 511 patients. All patients were referred for preoperative dental screening per protocol. Dental screening failure was defined as required dental intervention by the dentist. Screening failure rate was calculated for and logistic regression was used to evaluate the relationship between odds of screening failure and patient demographic data. Results In 94 of the 511 total cases (18.5%), patients failed dental screening and required dental procedures prior to TJA. Reasons for failure included tooth extractions, root canals, abscess drainage, and carious lesions requiring filling. Patient characteristics associated with failed dental screening included male gender (odds ratio 1.56, 95% confidence interval 1.0006-2.468, P = .047) and current smoker (odds ratio 3.6, 95% confidence interval 1.650-7.927, P = .001). Conclusion Universal dental screening prior to primary TJA resulted in 18.5% of patients needing an invasive dental intervention. Universal dental screening results in extra cost and time for patients and providers. Although male gender and active smoking were associated with increased odds of requiring an invasive dental procedure, more work is needed to develop targeted screening to improve perioperative workflow and limit unnecessary dental evaluations for patients.
States and the PPP: The Tax Policy Case for State Nondeductibility

This article is the second in a series evaluating the state tax aspects of the federal Paycheck Protection Program. The first article introduced the program and explained the potential effect on states if Congress were to change the law to allow taxpayers to deduct their PPP-funded expenses. This article continues that analysis and explores the tax policy reasons why states should prepare to deviate from federal law now that Congress has provided for PPP deductibility in its year-end COVID relief bill.
Influence of the primary and secondary coordination spheres on nitric oxide adsorption and reactivity in cobalt(II)–triazolate frameworks

Nitric oxide (NO) is an important signaling molecule in biological systems, and as such, the ability of porous materials to reversibly adsorb NO is of interest for potential medical applications. Although certain metal–organic frameworks are known to bind NO reversibly at coordinatively unsaturated metal sites, the influence of the metal coordination environment on NO adsorption has not been studied in detail. Here, we examine NO adsorption in the frameworks Co2Cl2(bbta) (H2bbta = 1H,5H-benzo(1,2-d:4,5-d′)bistriazole) and Co2(OH)2(bbta) using gas adsorption, infrared spectroscopy, powder X-ray diffraction, and magnetometry. At room temperature, NO adsorbs reversibly in Co2Cl2(bbta) without electron transfer, with low temperature data supporting spin-crossover of the NO-bound cobalt(II) centers of the material. In contrast, adsorption of low pressures of NO in Co2(OH)2(bbta) is accompanied by charge transfer from the cobalt(II) centers to form a cobalt(III)–NO− adduct, as supported by diffraction and infrared spectroscopy data. At higher pressures of NO, characterization data indicate additional uptake of the gas and disproportionation of the bound NO to form a cobalt(III)–nitro (NO2−) species and N2O gas, a transformation that appears to be facilitated by secondary sphere hydrogen bonding interactions between the bound NO2− and framework hydroxo groups. These results provide a rare example of reductive NO binding in a cobalt-based metal–organic framework, and they demonstrate that NO uptake can be tuned by changing the primary and secondary coordination environment of the framework metal centers.
Gene flow among vestimentiferan tube worm (Riftia pachyptila) populations from hydrothermal vents of the eastern Pacific

Allozyme data are presented for six discrete populations of the giant hydrothermal vent tube worm Riftia pachyptila Jones, 1981 collected throughout the species' known range along mid-ocean spreading ridges of the eastern Pacific Ocean. Contrary to an earlier report, levels of genetic variation are relatively high in this species. Estimates of gene flow based on F-statistics revealed that dispersal throughout the surveyed region is sufficiently high to counter random processes that would lead to losses of genetic diversity and significant population differentiation. R. pachyptila, like other species of tube worms, displays considerable morphologic variation among populations, but this diversity is not reflected in allozyme variation. Vestimentifera, in general, appear to show extensive phenotypic plasticity. In the light of the available genetic data, caution is warranted when making inferences about the taxonomic status of collections based on morphological variation alone. A general decrease in estimated rates of gene flow between geographically more distant populations supports the hypothesis that dispersal in this species follows a stepping-stone model, with exchange between neighboring populations in great excess of long-distance dispersal. High levels of gene flow have been recorded in a variety of vent fauna and may be a prerequisite for success of species found in the ephemeral habitats associated with regions of sea-floor hydrothermal activity.
Generation of chordoma cell line JHC7 and the identification of Brachyury as a novel molecular target: Laboratory investigation

Object Chordoma is a malignant bone neoplasm hypothesized to arise from notochordal remnants along the length of the neuraxis. Recent genomic investigation of chordomas has identified T (Brachyury) gene duplication as a major susceptibility mutation in familial chordomas. Brachyury plays a vital role during embryonic development of the notochord and has recently been shown to regulate epithelial-to-mesenchymal transition in epithelial-derived cancers. However, current understanding of the role of this transcription factor in chordoma is limited due to the lack of availability of a fully characterized chordoma cell line expressing Brachyury. Thus, the objective of this study was to establish the first fully characterized primary chordoma cell line expressing gain of the T gene locus that readily recapitulates the original parental tumor phenotype in vitro and in vivo. Methods Using an intraoperatively obtained tumor sample from a 61-year-old woman with primary sacral chordoma, a chordoma cell line (JHC7, o...
Assessing Custodial Mother Adjustment to Divorce

Abstract This study assesses divorce adjustment of custodial mothers. Measures designed to assess psychological functioning of the custodial mother and family functioning are employed. Fifty-six custodial mothers completed the assessment measures. The results indicate that custodial mothers who report healthier levels of overall family functioning on the Divorce Adjustment Inventory-Revised (DAI-R), demonstrate healthier levels of psychological functioning as assessed by the Symptom Checklist 90-Revised (SCL-90-R) than custodial mothers who report lower levels of overall family functioning. In addition, divorce education (Families in Transition) participants had better family conflict and resolution skills, more favorable divorce conditions, and a more positive view of the divorce transition at the end of the program than did nonparticipants (DAI-R scale scores). Overall, these results provide a baseline for reported symptomatology among divorced women, confirm the efficacy of a divorce education program ...
Accounting for Selection and Mating Biases in Genetic Evaluations

When selection has occurred, the means and variances of random variables are different from those under the usual assumptions of mixed linear models. Consequently, the solution to regular mixed model equations sometimes gives biased estimators and predictors. Given multivariate normal distributions and a vector variable used to make selection and mating decisions, the mixed model equations can be modified to yield unbiased estimators and predictors. This modification is described and several examples are given of its application, including cow culling, selection on records not available for analysis, estimation of genetic and environmental trends, association between sire and herd values, genetic groups, differential treatment, and assortative mating with and without selection.
Effects of Plasma Mass Flow on Alfven Wave Phase Mixing in Coronal Loops

Ground-based and space observations suggest that flow phenomena are intrinsic to the solar corona loops. The present analysis addresses flow effects on Alfven wave behavior in coronal loops. The effect of flow on the shear Alfven wave continuum and the associated damping process resulting from phase-mixing is investigated. Flow Doppler-shifts the Alfven wave continuum, thus displacing the range of frequencies for optimum heating. The present study explores Alfven resonance effects on surface waves propagating along coronal loops that are under the influence of flow. Coupling to the Alfven resonance leads to damping of the surface waves. The damping rate in the presence of sub-Alfvenic flows is computed. Flow increases the damping rate of certain modes, thus enhancing the heating effectiveness of those modes. Therefore, these calculations suggest that flow is potentially an important ingredient for an accurate evaluation of heating the solar corona by dissipation of Alfven waves via phase-mixing.
Simple method for concentration of bacteria from large volumes of tap water

Membrane adsorption-elution techniques have made it possible to concentrate and detect small numbers of viruses in large volumes of water and wastewater, but no such methods are available for quantitative recovery of bacteria. A number of waterborne disease outbreaks of "unknown etiology" in the United States are suspected to have been caused by pathogens present in numbers too small to be detected by currently available methodology. The present study reports on the use of positively charged depth filters for the concentration and detection of bacteria in large volumes of tap water. In this method, dechlorinated tap water was passed, under positive pressure, through positively charged filter media (Zetaplus, 05S). More than 90% of seeded bacteria adsorbed to these filters at ambient pH levels. Adsorbed bacteria were eluted by passing a small volume of Trypticase soy broth in the direction opposite of the influent flow. By this method, Escherichia coli and Salmonella serovar B organisms in 20 liters of tap water were concentrated in a final volume of 50 ml, with an average recovery efficiency of greater than or equal to 30%.
Facing Age: Women Growing Older in an Anti-Aging Culture, by Laura H. Clarke

Dr. Clarke's book is the first in the series Diversity in Aging published by Rowman & Littlefield. The series editor is Toni Calasanti, PhD. Dr. Clarke's research interests include a focus on aging...
Glycolic Acid Peels for Postinflammatory Hyperpigmentation in Black Patients: A Comparative Study

BACKGROUND Treatment of postinflammatory hperpigmentation in patients of Fitzpatrick skin types TV, V, and VI is difficult, Glycolic acid peels are useful for pigment dyschromias in Caucasians; however, there are no controlled studies examining their safety and efficacy in dark-complexioned individuals. objective. To determine if serial glycolic acid peels provide additional improvement when compared with a topical regimen of hydroquinone and tretinoin. METHODS Nineteen patients with Fitzpatrick skin type IV, V, or VI were randomized to a control or peel group. The control group applied 2% hydroquinone/10% glycolic acid get twice daily and 0.05% tretinoin cream at night. The peel patients used the same topical regimen and, in addition, received six serial glycolic acid peels (68% maximum concentration). Patients were evaluated with photography, colorimetry, and subjectively. RESULTS Sixteen patients completed the study. Both treatment groups demonstrated improvement, but the patients receiving the glycolic acid peels showed a trend toward more rapid and greater improvement. The peel group also experienced increased lightening of the normal skin. CONCLUSIONS This pilot study demonstrates that serial glycolic acid peels provide an additional benefit, with minimal adverse effects, for the treatment of postinflammatory hyperpigmentation in dark-complexioned individuals.
Hormones in human reproduction

Abstract Following the administration of progesterone labeled with carbon 14 at position 21 to a patient with a normal pregnancy about 70 per cent of the administered radioactivity was recovered from the urine, feces, and expired air (22.62 per cent, 29.74 per cent, and 18.56 per cent, respectively). The excretion of radioactive metabolites by the skin was minimal. At present we have not accounted for the remaining 30 per cent of the administered radioactivity, but it seems likely that part of it is stored in the fat compartments of the body for a considerable length of time. There was no relationship between the urinary recovery of radioactivity and the pregnant and nonpregnant state, nor the viability of the fetus. The metabolites in urine and feces consist mainly of conjugated steroids, as pregnanediol, pregnanolone, and other unknown compounds. The elimination of tagged carbon dioxide after the administration of C 14 -21-progesterone indicates an oxidation of the side chain of the progesterone molecule, resulting in the formation of such steroids as androstenedione and related compounds which have androgenic properties. Determinations of radioactivity in the blood plasma following the intravenous and intramuscular administration of the labeled hormone demonstrated a rapid disappearance of the free steroid from the circulation due to (1) a speedy conjugation with glucuronic acid and (2) rapid diffusion into body tissues, mainly into the fat compartment. In contrast to the high concentration of radioactivity in the fat, only moderate amounts of radioactivity were demonstrated in the myometrium and the decidua of pregnant patients. Extremely low concentrations of radioactivity were found in the endometrium of non-pregnant women during the pre- and postovulatory phases of the menstrual cycle, and no radioactivity was demonstrable in the atrophic endometrium of 2 patients. The absence of estrogenic activity seems to prevent the entrance of the hormone into the cells of the mucosal layer of the uterus. This observation provides direct evidence that estrogens must prepare the endometrial cells in order that progesterone can exhibit its progestational effect. Apparently, only minimal amounts of progesterone and/or its metabolites are necessary to exert its biological effects on the endometrium. Preliminary studies on the biosynthesis of estrogens in human pregnancy revealed that cholesterol as well as testosterone can serve as a precursor of estrone. In a patient with choriocarcinoma C 14 -4-progesterone was converted into radioactive estrone. The data which we have presented here complete another milestone in the very long experimental road toward our understanding of the metabolism and biosynthesis of the steroid hormones in mammalian reproduction. It becomes increasingly apparent that our thorough understanding of their role in the normal reproductive process must precede an intelligent approach to the solution of many problems in obstetrics and gynecology.
When it is Embedded, it is Potent: Effects of General Attitude Embeddedness on Formation of Specific Attitudes and Behavioral Intentions

Attitude embeddedness, defined as the degree of connectedness of an attitude to other cognitive elements, was operationalized as the number of free associations subjects produced in relation to the attitude issue. Two experiments demonstrated that embeddedness moderated the effects of general attitudes on specific attitudes in situations that were ambiguously related to general attitudes. Highly embedded general attitudes but not low-embedded general attitudes toward capital punishment or the right to die served as a basis for the formation of specific evaluations of situations that were only moderately relevant for the broader issue. A third experiment demonstrated that highly embedded attitudes toward preservation of the environment were more strongly related to behavioral intentions than low-embedded attitudes were.
Oxide dispersion-strengthened steels: A comparison of some commercial and experimental alloys

Oxide dispersion-strengthened (ODS) steels are being developed and investigated for nuclear fission and nuclear fusion applications in Japan, Europe, and the United States. In addition, commercial ODS products are available and have been used in niche applications. Microstructural and mechanical properties studies have been conducted at Oak Ridge National Laboratory and elsewhere on various commercial and experimental ODS steels. Tensile and creep properties have been obtained and collected from literature and commercial sources. These data are compared to show the differences and similarities of different ODS steels, and observations are explained in terms of the microstructures of the steels.
An anomalous M1 transition in 38Cl

Abstract The observed enchangement of the M1 transition in 38Cl between the 3− state of the “ d 3 2 - p 3 2 multiplet” and the 4− state of the “ d 3 2- f 7 2 mumultiplet” is explained.
A Mathematical Model for Timing the Release from Sequestration and the Resultant Brownian Migration of SeqA Clusters in E. coli

DNA replication in Escherichia coli is initiated by DnaA binding to oriC, the replication origin. During the process of assembly of the replication factory, the DnaA is released back into the cytoplasm, where it is competent to reinitiate replication. Premature reinitiation is prevented by binding SeqA to newly formed GATC sites near the replication origin. Resolution of the resulting SeqA cluster is one aspect of timing for reinitiation. A Markov model accounting for the competition between SeqA binding and methylation for one or several GATC sites relates the timing to reaction rates, and consequently to the concentrations of SeqA and methylase. A model is proposed for segregation, the motion of the two daughter DNAs into opposite poles of the cell before septation. This model assumes that the binding of SeqA and its subsequent clustering results in loops from both daughter nucleoids attached to the SeqA cluster at the GATC sites. As desequestration occurs, the cluster is divided in two, one associated with each daughter. As the loops of DNA uncoil, the two subclusters migrate apart due to the Brownian ratchet effect of the DNA loop.
Asymptotics of Eigenvalues for Sturm-Liouville Problems with an Interior Singularity

We consider the asymptotic form of the eigenvalues of the linear differential equation −y″(x) + q(x) y(x) = λ y(x), −∞ < a < x < b < ∞, where a < 0 < b, q(x) is singular at x = 0, and y satisfies appropriate conditions at a, 0, and b. This extends previous work of Atkinson and of Harris. In particular, when q(x) = x−K, Atkinson derived asymptotic formulae which cover the case 1 ≤ K < 43; Harris′s results cover the cases 1 ≤ K < 32. We now cover all of the cases 1 ≤ K < 2. Since the methods employed by both of these authors and ourselves apply only to limit circle, non-oscillatory expressions, our results now seem to take problems of this type to their conclusion.
Third-order distortion elimination in phase-encoded analog-photonic links using a four-wave mixing comb source

We present all-optical distortion cancellation in phase-modulated analog-photonic links by combining the phase-encoded signal with lines from an optical comb generated from signal. Experimentally, we fully cancel third-order distortion increasing the link SFDR by >8.3dB.
An experimental study of surface cooling by bubbles during nucleate boiling of water

By using a special surface thermocouple Moore and Mesler have measured large temperature fluctuations during nucleate boiling of water on chromel P surface. They found that the temperature dropped 20° to 30°F. in about 2 msec. but required 10 to 20 msec. to recover. They have postulated that the surface was cooled during initial bubble growth by evaporation of a microlayer into the bubble. To test this hypothesis a technique was developed to photograph a bubble growing from an artificial site as the surface temperature was measured. Temperature fluctuations were recorded on an oscilloscope which automatically triggered the bubble photographs by means of a time delay unit and flash tube. Photographs of bubbles were taken at 1 μsec. exposure time and ranged from about 10 μsec. after the start of the temperature drop to about 1 msec. before the start of another cycle. The photographs show that the surface cools during bubble growth and recovers during bubble departure.
Nephrogenic adenoma associated with interstitial cystitis

A nephrogenic adenoma occurring in a forty-five-year-old male with a past history of urinary tract infection and interstitial cystitis is described. Four years after the diagnosis of interstitial cystitis, nephrogenic adenoma developed. The patient underwent a total cystoprostatectomy and urinary diversion for bilateral vesicoureteral reflux and progressive and incapacitating symptoms that persisted in spite of accepted standards of management for this disease. This case further supports the role of chronic inflammatory processes of the bladder in the subsequent development of nephrogenic adenoma.
Optical Constants of Clean Titanium and Tungsten Surfaces as Functions of Temperature

The optical constants of single-crystal Ti (0001) and W (110) and polycrystalline W and Ti have been measured as functions of temperature at two wavelengths (5461 and 6328 A). The crystals were cleaned by ion bombardment and annealed to remove surface damage and bombardment impurities. The degree of surface contamination was monitored by Auger spectroscopy.
Age-specific growth rates: the legacy of past population dynamics.

Recent developments in population mathematics have focused attention on a function that is widely available but rarely examined: the set of age-specific growth rates in a population. In particular, this set of rates is sufficient for translating the current birth rate and age-specific mortality rates into the current age distribution. This growth-rate function contains all of the pertinent features of a population’s demographic history that are required to relate major demographic functions for a particular period to one another. This article presents an expression fm the age-specific growth rate and uses it to derive an equation for age distribution. We show how the value of the age-specific growth rate is determined by a population’s demographic past and present various sets of growth rates corresponding to stylized demographic scenarios. Several noteworthy sets of growth rates observed in human populations are discussed. Finally, we explain why age-specific growth rates make it possible to determine the age distribution solely from information on current demographic conditions.