CyVerse: Cyberinfrastructure for open science

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.

Speech-Language Pathology Practices for Adults With Right Hemisphere Stroke: What Are We Missing?

Purpose Limited evidence exists to guide the assessment and treatment of cognitive-communication disorders associated with right hemisphere stroke. The purpose of this study was to obtain information about speech-language pathologists' (SLPs') clinical practices and decision making for this population to understand what practices are being used and identify gaps in clinical practice. Method A survey was distributed via online ASHA Communities for the Special Interest Groups and other social media platforms. Respondents included 143 SLPs from across the United States representing 3-50 years of experience and a wide range of practice settings. Survey questions probed assessment practices including how tests are selected, what tests are used to diagnose specific deficits, and how confident SLPs were in their diagnoses. Treatment decisions were queried for a small set of disorders. Results SLPs routinely assess cognitive disorders using standardized tests. Communication disorders are less likely to be formally assessed. Three core right cerebral hemisphere deficits-anosognosia, aprosodia, and pragmatic deficits-are either not assessed or assessed only through observation by 80% of SLPs. Evidence-based treatments are commonly used for disorders of attention, awareness, and aprosodia. Conclusion Communication disorders are less likely to be formally assessed than cognitive disorders, creating a critical gap in care that cannot be filled by other allied health professionals. Suggestions for free or low-cost resources for evaluating pragmatics, prosody, and awareness are provided to aid SLPs in filling this gap. Supplemental Material https://doi.org/10.23641/asha.12159597.

FGF2 Induces Migration of Human Bone Marrow Stromal Cells by Increasing Core Fucosylations on N-Glycans of Integrins

Since hundreds of clinical trials are investigating the use of multipotent stromal cells (MSCs) for therapeutic purposes, effective delivery of the cells to target tissues is critical. We have found an unexplored mechanism, by which basic fibroblast growth factor (FGF2) induces expression of fucosyltransferase 8 (FUT8) to increase core fucosylations of N-linked glycans of membrane-associated proteins, including several integrin subunits. Gain- and loss-of-function experiments show that FUT8 is both necessary and sufficient to induce migration of MSCs. Silencing FUT8 also affects migration of MSCs in zebrafish embryos and a murine bone fracture model. Finally, we use in silico modeling to show that core fucosylations restrict the degrees of freedom of glycans on the integrin's surface, hence stabilizing glycans on a specific position. Altogether, we show a mechanism whereby FGF2 promotes migration of MSCs by modifying N-glycans. This work may help improve delivery of MSCs in therapeutic settings.

Confidence interval prediction for neural network models

To derive an estimate of a neural network's accuracy as an empirical modeling tool, a method to quantify the confidence intervals of a neural network model of a physical system is desired. In general, a model of a physical system has error associated with its predictions due to the dependence of the physical system's output on uncontrollable or unobservable quantities. A confidence interval can be computed for a neural network model with the assumption of normally distributed error for the neural network. The proposed method accounts for the accuracy of the data with which the neural network model is trained.

Decoding the ancient Greek astronomical calculator known as the Antikythera Mechanism

The Antikythera Mechanism is a unique Greek geared device, constructed around the end of the second century bc. It is known that it calculated and displayed celestial information, particularly cycles such as the phases of the moon and a luni-solar calendar. Calendars were important to ancient societies for timing agricultural activity and fixing religious festivals. Eclipses and planetary motions were often interpreted as omens, while the calm regularity of the astronomical cycles must have been philosophically attractive in an uncertain and violent world. Named after its place of discovery in 1901 in a Roman shipwreck, the Antikythera Mechanism is technically more complex than any known device for at least a millennium afterwards. Its specific functions have remained controversial because its gears and the inscriptions upon its faces are only fragmentary. Here we report surface imaging and high-resolution X-ray tomography of the surviving fragments, enabling us to reconstruct the gear function and double the number of deciphered inscriptions. The mechanism predicted lunar and solar eclipses on the basis of Babylonian arithmetic-progression cycles. The inscriptions support suggestions of mechanical display of planetary positions, now lost. In the second century bc, Hipparchos developed a theory to explain the irregularities of the Moon's motion across the sky caused by its elliptic orbit. We find a mechanical realization of this theory in the gearing of the mechanism, revealing an unexpected degree of technical sophistication for the period.

Booster seat use and reasons for nonuse

BACKGROUND

Many children 4 to 9 years old are inappropriately restrained in vehicles and are at risk for injury in crashes.

OBJECTIVES

This study was undertaken to determine the rate of booster seat use and the reasons for nonuse.

METHODS

Observations were conducted at a random sample of day care centers, and drivers of unrestrained children 4 to 8 years old were interviewed to determine the reasons for lack of booster seat use.

RESULTS

Observations were conducted on 149 children. Shoulder belt use significantly increased with the age of the child; 28.3% of 4-year-olds and 70.0% of 6- to 8-year-olds used lap-shoulder belts. Overall, 27.7% of children in the target age group used booster seats; only 10% of children 6 to 8 years old were restrained with booster seats. Booster seat use decreased when there were 3 or more passengers in the vehicle. The most common reason for lack of booster seat use was that parents thought the child was large enough to use the regular lap-shoulder belt system, or problems with attempting to use the seat in the vehicle. More than one half of parents who were not using booster seats at the time of the survey reported owning seats.

CONCLUSION

This study indicates that parental misconceptions about size and safety of regular restraint equipment are the most common reason that children are not appropriately restrained in vehicles. This information can be used to guide community intervention programs.

Managing the care of complex, difficult patients in the medical-surgical setting

The increasing medical, psychological, and social complexity of hospitalized patients is a serious concern. Most staff nurses are inadequately prepared to deal with the complexity of these patient's issues. The difficult patient is described as having a medical condition requiring hospitalization and who also exhibits problems such as pain, substance abuse, and issues such as anger, manipulation, or noncompliance which are difficult and challenging behaviors. An overview of the most troublesome patients seen in the inpatient setting today and some clinical direction on how to best manage these patients are presented.

Self-reported narcissism and perceived parental permissiveness and authoritarianism

The hypothesis that inadequate parenting promotes the development of pathological narcissism was tested in a sample of 370 undergraduate students. They responded to the O'Brien (1987) Multiphasic Narcissism Inventory (OMNI) and to measures of parental permissiveness, authoritarianism, and authoritativeness. Perceived parental permissiveness and authoritarianism served as independent predictors of greater narcissistic tendencies. The students who scored high on the OMNI were also less likely to evaluate both of their parents as having been especially strong in their use of the adjustment-promoting authoritative style. Theoretical efforts to link narcissism with inadequate parenting therefore may have merit and may deserve additional research attention.

Further contrasts between self-reflectiveness and internal state awareness factors of private self-consciousness

Although widely used as a unitary measure of self-focused attention, the Private Self-Consciousness subscale (Fenigstein, Scheier, & Buss, 1975) contains two factors. In the present study, this subscale and its self-reflectiveness (SR) factor predicted greater shame, guilt, other-directedness, and social anxiety; but the internal state awareness (ISA) factor displayed relationships that were in the opposite direction. Contrasts between SR and ISA often became more obvious in partial correlations, when one factor was examined while controlling for the other. In relationships with personal and social identity, SR appeared to reflect public as much as private self-consciousness. These data support recent suggestions that it may be necessary to construct more adequate measures of private self-consciousness.

Characterisation of the copper uptake mechanism and isolation of the ceruloplasmin receptor/copper transporter in human placental vesicles

In this paper we have studied copper (Cu) uptake by microvillar vesicles isolated from human term placenta. We have characterised Cu uptake from CuHis2 complexes and shown that ceruloplasmin (Cp) inhibits uptake. Inhibition is complex and variable; in one series of experiments, the Vmax for uptake drops from 31.3 +/- 1.2 nmol/min per mg vesicle protein without added Cp to 11.3 +/- 1 nmol/min per mg vesicle protein at 91 micrograms/ml Cp. Similarly, the K0.5 increases from 0.35 +/- 0.08 microM to 1.35 +/- 0.25 microM, while the n value (the Hill coefficient) falls from 1.9 +/- 0.23 in the absence of Cp to 1.1 +/- 0.13 In another series, Cp had no effect below concentrations of about 100 micrograms/ml and in a third series only increased K0.5. The variability in effect seems to be related to the specific activity of the ceruloplasmin, which in turn is related to the copper complexes of the protein. The effect is specific for Cp; apotransferrin and a2-macroglobulin have no effect. 67Cu-labelled ceruloplasmin binds specifically to vesicles of term placenta with an affinity of 2.8 microU/mg vesicle protein and a Bmax of 79 microU/mg vesicle protein. CuHis2, but not histidine alone, can block the uptake. The data can be reconciled by proposing that the binding site of the transporter is relatively small and recognises a Cu-dihistidine structure common to the low-molecular-weight complex and to the Type I and Type II coppers of ceruloplasmin. We have used these observations to develop an isolation method for the transporter and have identified it as a protein of M(r) 90,000 which is closely associated with alkaline phosphatase. There are also two proteins of M(r) 45,000 and 40,000 which may be breakdown products of the larger complex. Antibodies to the 45,000 protein block Cu binding and uptake from CuHis2 complexes, strongly implicating it as the copper transporter/ceruloplasmin receptor of human term placenta.

Chemical reactivity of some isothiazolone biocides

Chemical reactions between the isothiazolone biocides, N-methylisothiazol-3-one (MIT), benzisothiazol-3-one (BIT) and 5-chloro-N-methylisothiazol-3-one (CMIT) with cysteine have been investigated by u.v. and NMR spectroscopy. At physiological pH all three agents interacted oxidatively with thiols to form disulphides. Further interaction with thiols caused the release of cystine and formation of a reduced, ring-opened form of the biocide (mercaptoacrylamide). In an analogous fashion to the initial reaction the mercaptoacrylamide reacted with another molecule of biocide to give biocide dimers. NMR spectral studies indicated that for CMIT the mercaptoacrylamide form is capable of tautomerization to a highly reactive thio-acyl chloride. Formation of mercaptoacrylamide was in all cases highly pH-dependent. Alcohol dehydrogenase was insensitive to all three agents but was highly sensitive to CMIT when co-administered with dithiothreitol. Capacity to form a thioacyl chloride from the mercaptoacrylamide is suggested to account for much of this enhanced activity. Stopped-flow spectroscopic studies showed rates of reaction with glutathione (GSH) to directly parallel antimicrobial activity. Additionally, CMIT was able to react directly with both ionization states of GSH (pH 7-10) whilst BIT and MIT appeared only to interact when the glutamyl-nitrogen of GSH was charged (pH 8.5).

Rearrangement of the T-cell-receptor beta-chain gene in the diagnosis of lymphoproliferative disorders

The arrangement of the T-cell-receptor and immunoglobulin genes has been analysed in 77 cases of lymphoproliferative disorder. All 6 T-cell leukaemias and 16 of 19 T-cell lymphomas showed rearrangement of the gene coding for the beta chain of the T-cell receptor, associated in all cases with a germline arrangement of the immunoglobulin genes. All 36 B-cell leukaemias and all 16 B-cell lymphomas showed rearrangement of immunoglobulin genes; the T-cell-receptor gene was in the germline configuration in most of these cases but showed a rearranged pattern in 3 cases (2 chronic lymphatic leukaemias and 1 immunoblastic lymphoma). The combined use of T-cell-receptor and immunoglobulin gene probes promises to be a valuable means of identifying and classifying T-cell neoplasms.

Insulin tolerance test: human growth hormone response and insulin resistance in primary unipolar depressed, bipolar depressed and control subjects

Preliminary data from the National Institute of Mental Health-Clinical Research Branch Collaborative Program on the Psychobiology of Depression dealing with the human growth hormone (hGH) response to the Insulin Tolerance Test (ITT) during the pre-treatment (drug-free) period of the study are presented in this paper. Data are reported for 54 unipolar depressed, 21 bipolar depressed, and 40 normal control subjects, who represent approximately 50% of the final subject sample to be studied. In this population the unipolar depressed subjects showed a significantly greater resistance to insulin-induced hypoglycaemia than bipolar and control subjects. After applying the inclusion/exclusion criteria necessary to interpret hGH responses accurately, the data from only 54 subjects were acceptable. Mean peak hGH concentrations were not significantly different among the three groups. There was, however, a significant difference in the distributions of the hGH peak response, with the bipolar depressed population demonstrating greater variability in response than unipolar and control populations. These findings are discussed as they relate to previous reports and theoretical considerations.

The biological fate of sulphur colloid

The in-vivo behaviour of sulphur colloid has been investigated using colloids labelled with 35S as well as 99m Tc. The rates of clearance of 35S and 99m Tc from the blood, the rates of accumulation in liver and bone and the distribution of the two radioisotopes in various organs are all markedly different. The results demonstrate that although technetium is rapidly removed from the blood stream and primarily accumulated in the liver the colloid particles themselves are broken down in vivo with the release of sulphur.

The physical and chemical characteristics of sulphur colloids

The characteristics of sulphur colloids have been investigated using colloids labelled with 35S as well as with 99mTc. The results support a model in which technetium is incorporated in the body of the particle rather than on its surface. Elemental sulphur on the surface of the particle is susceptible to attack both by sulphide ions and by protein and other materials containing --SH groups. The ready conversion of sulphur to soluble polysulphides means that sulphur colloid particles undergo conspicuous changes in diameter, both while standing in a closed vial, and on injection into body fluids. This behaviour casts doubts on the value of routine particle-size measurement as a quality control procedure.