cssi/SciSciGPT-SciSciNet huggingface dataset:
Analysis of knowledge‐based protein‐ligand potentials using a self‐consistent method

We propose a self-consistent approach to analyze knowledge-based atom-atom potentials used to calculate protein-ligand binding energies. Ligands complexed to actual protein structures were first built using the SMoG growth procedure (DeWitte & Shakhnovich, 1996) with a chosen input potential. These model protein-ligand complexes were used to construct databases from which knowledge-based protein-ligand potentials were derived. We then tested several different modifications to such potentials and evaluated their performance on their ability to reconstruct the input potential using the statistical information available from a database composed of model complexes. Our data indicate that the most significant improvement resulted from properly accounting for the following key issues when estimating the reference state: (1) the presence of significant nonenergetic effects that influence the contact frequencies and (2) the presence of correlations in contact patterns due to chemical structure. The most successful procedure was applied to derive an atom-atom potential for real protein-ligand complexes. Despite the simplicity of the model (pairwise contact potential with a single interaction distance), the derived binding free energies showed a statistically significant correlation (approximately 0.65) with experimental binding scores for a diverse set of complexes.
Desiccation tolerance of protoplasts isolated from pea embryos.

To facilitate studies of desiccation tolerance at the cellular level, a technique to isolate protoplasts from desiccation-tolerant pea (Pisum sativum L. cv. Alaska) embryos has been developed. Using FDA (fluorescein diacetate) as a probe, viability of the protoplasts was investigated before and after drying to determine whether the protoplasts could survive desiccation in a manner similar to the tissue from which they were isolated. Protoplasts were isolated from 12 h imbibed pea axes, suspended in several different sugar solutions, then dried to water contents less than 0.2 g H 2 O g 1 DW. Protoplasts only survived drying if the rate was rapid (< 2 h), while slow drying (24 h) was lethal. Maximal survival (75%) was obtained after drying protoplasts with a mixture of sucrose and raffinose, while pure sucrose and trehalose were somewhat less effective protectants. Low survival was obtained after drying protoplasts with monosaccharides and pure raffinose. Protoplasts isolated from germinated seedlings did not survive dehydration below 0.2 g H 2 O g -1 DW. Transmission electron microscopy revealed that dried desiccation-tolerant protoplasts appeared shrunken, with folded membranes, while dried protoplasts from sensitive tissue had disrupted membranes. While isolated protoplasts maintained some of the desiccation tolerance of orthodox seeds, their inability to survive complete drying and their sensitivity to drying rate is similar to the behaviour of recalcitrant embryos.
Patches of Disorganization in the Neocortex of Children with Autism

Background Autism involves early brain overgrowth and dysfunction, which is most strongly evident in the prefrontal cortex. As assessed on pathological analysis, an excess of neurons in the prefrontal cortex among children with autism signals a disturbance in prenatal development and may be concomitant with abnormal cell type and laminar development. Methods To systematically examine neocortical architecture during the early years after the onset of autism, we used RNA in situ hybridization with a panel of layer- and cell-type– specific molecular markers to phenotype cortical microstructure. We assayed markers for neurons and glia, along with genes that have been implicated in the risk of autism, in prefrontal, temporal, and occipital neocortical tissue from postmortem samples obtained from children with autism and unaffected children between the ages of 2 and 15 years. Results We observed focal patches of abnormal laminar cytoarchitecture and cortical disorganization of neurons, but not glia, in prefrontal and temporal cortical tissue from 10 of 11 children with autism and from 1 of 11 unaffected children. We observed heterogeneity between cases with respect to cell types that were most abnormal in the patches and the layers that were most affected by the pathological features. No cortical layer was uniformly spared, with the clearest signs of abnormal expression in layers 4 and 5. Three-dimensional reconstruction of layer markers confirmed the focal geometry and size of patches. Conclusions In this small, explorative study, we found focal disruption of cortical laminar architecture in the cortexes of a majority of young children with autism. Our data support a probable dysregulation of layer formation and layer-specific neuronal differentiation at prenatal developmental stages. (Funded by the Simons Foundation and others.)
On construction of bandwidth efficient, low complexity, and high coding gain 8-PSK modulation codes

Nested concatenated coded 8-PSK (phase-shift keying) modulation schemes are proposed to achieve good error performance, large coding gains, and high spectral efficiency with reduced decoding complexity. In the concatenation, Reed-Solomon (RS) codes, including the NASA standard (255,223) RS code, are used as the outer codes and multidimensional trellis 8-PSK codes are used as the inner codes. The inner codes are constructed from convolutional codes with good free branch distances and multidimensional 8-PSK coset codes through concatenation. Analytical and simulation results show that these schemes perform extremely well and achieve impressive coding gains over uncoded reference systems for bit error rates below 10/sup -3/. These schemes achieve large coding gains with reduced decoding complexity. >
DIFFERENCES BETWEEN FISHERY‐DEPENDENT AND FISHERY‐INDEPENDENT ESTIMATES OF SINGLE‐AND MIXED‐SPECIES DOLPHIN SCHOOLS: IMPLICATIONS FOR SINGLE‐SPECIES STOCK ASSESSMENTS

Since 1979, fishery-independent data and fishery-dependent data have been used to estimate trends in the abundance of the northeastern stock of spotted dolphins in the eastern tropical Pacific. Data collected aboard tuna vessels have been used to estimate trends in relative abundance, while data collected from fishery-independent research vessels have been used to estimate trends in actual abundance. One of the largest discrepancies between the two data sources is that tuna vessels tend to report dolphin schools that are 400%-500% larger than schools observed by research vessels. After comparing research vessel and tuna vessel observations overlapping in space and time, it appears that either measurement error or selective reporting of large schools is the most likely explanation for the disparity. Comparing single-species schools against portions of mixed-species schools introduced bias. Revised fishery-dependent abundance estimates were generated using only single-species dolphin schools, resulting in estimates that appear more similar to recent fishery-independent abundance estimates. Biases associated with mixed-species schools did not appear to be correctable in fishery-dependent data, suggesting that data on mixed-species schools should not be considered if fishery-dependent data are to be combined with fishery-independent data for stock assessment purposes.
An economic analysis of energy generation and food waste diversion for enhanced biogas production at a colorado wastewater treatment facility

Food waste diversion to enhance biogas production for energy generation in municipal wastewater treatment plants (WWTPs) is an emerging trend in the United States. Using an interested WWTP in Fort Collins, Colorado a study was completed to determine the efficacy and viability of implementing a food waste diversion program utilizing food waste as a feedstock in their existing anaerobic digesters to enhance biogas production. The results of the study concluded that a food waste diversion program would result in a loss of approximately $2.5 million over a 20 year period making the program unfeasible currently. However, the use of excess biogas produced in the plant9s anaerobic digesters from the processing of the municipal solid waste stream (MSW) to fuel a reciprocating engine energy generation technology would result in an estimated return on investment of $1.63 million, and an estimated return on investment of $1.25 million for a microturbine energy generation technology over the same 20 year time period. Changes to multiple variables in the economic analysis such as higher energy costs and higher landfill tipping fees could result in a more positive outlook for a future food waste diversion program in Northern Colorado. This study can be used by other WWTPs in the US and other countries as a model to determine the initial economic feasibility of a food waste diversion program in their area. WWTPs in locations with greater costs associated with energy and tipping fees than those reported in this study may find a food waste diversion program economically viable and beneficial.
Critical behavior in spallation failure of metals

Using molecular dynamics with an accurate many-body potential, we studied the rapid expansion of Ta metal following the high compression (50 to 100 GPa) induced by high velocity (2 to 4 km/s) impact. We find that catastrophic failure in this system coincides with a critical behavior characterized by a void distribution of the form N(v)∝V-τ, with τ∼2.2. This corresponds to a threshold in which percolation of the voids results in tensile failure. We define an order parameter (φ, the ratio of the volume of the largest void to the total void volume) which changes rapidly from ∼0 to ∼1 when the metal fails and scales with as φ∝(ρ-ρc)β with exponent β∼0.4, where ρ is the total void fraction. We found similar behavior for FCC Ni suggesting that this critical behavior is a universal characteristic for failure of solids in rapid expansion.
Pre-selection of B-Lymphocytes by Antigen for Fusion to Myeloma Cells by Pulsed Electric Field (PEF) Method

Cells treated with pulsed electric field (PEF) tend to fuse together when brought into close contact by various means. The original discovery of this phenomenon is hard to trace because of the lack of documentation. Early findings of cells fused into large aggregates or mass by PEF were not fully appreciated and, therefore, few serious efforts were made to investigate the underlying biophysical mechanisms causing cell membrane fusion. It is quite possible that the value of electrofusion in biology and medicine were not fully realized by pioneering physicists. Evidently, several investigators and their coworkers continued with this research and are responsible for the recent resurrection of pulsed electric field method to induce cell fusion (Zimmermann et al., 1985; Neumann et al., 1980;Tsong, 1983;Teissie et al., 1982;Lo et al., 1984). Their championing of the potential applications of this technology in genetics and agriculture, and their experiments have contributed to recent interest paid by molecular and cell biologists alike to the PEF method (see e.g. chapters by Zimmermann, Sowers, Hui and Lucy). Another related area of current excitement, namely, the electric perforation of cell membranes for loading gene material, DNA, into cells has also helped to gain the popularity of the PEF method (Neumann et al., 1982; Potter et al., 1984; Tsong, 1983). Cell fusion using PEF is relatively simple.
Hybrid ZnO/SWNT Nanostructures Based Gas Sensor

Zinc oxide (ZnO) nanoparticles decorated single walled carbon nanotubes (SWNTs) were electrochemically synthesized where the deposition conditions were systematically explored to tailor the size, density, and microstructure of the ZnO nanoparticles and correlated to the gas sensing performance. Room temperature conductometric detection of various analytes including CO, CO2, NO2, NH3, SO2, H2S with ZnO/SWNT hybrid nanostructures demonstrated uncharacteristic selectivity towards H2S with little to no response for the other analytes examined. Optimal ZnO/SWNTs gas sensor devices showed a significantly increased in H2S sensitivity over unfunctionalized SWNT networks (i.e. 4.96 % per ppmV vs. 0.225 % ppmV) with a lower detection limit in the ppb range. Additionally, the H2S sensing performance was greatly improved by enhancing the crystallinity of ZnO nanoparticles.
Teaching computer systems performance analysis

A course on computer systems performance analysis has been adapted for several different distance education delivery options, including an interactive television system, face-to-face presentation at a satellite campus, and delivery over the Internet to independent study students. Of the 122 students who have enrolled in this graduate-level course for a grade over the three-year period analyzed, half have been nontraditional students who never set foot on campus. These remote students have a substantially higher drop-out rate than the traditional on-campus students, and frequently indicate a strong preference for face-to-face instruction in a traditional classroom setting. Nevertheless, due to significant differences in the characteristics of the two student groups, the remote students typically earn higher final course grades than the on-campus students. While there is a strong demand for delivery of this type of advanced course to remote students, more still needs to be done to effectively engage these students in the learning process.
Verification and Sensitivity Experiments for the WISP94 MM5 Forecasts

Abstract A statistical verification of real-time forecasts from the Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model version 5 (MM5) examines several model biases noted in numerical forecasts prepared for the Winter Icing and Storms Project’s 1994 field experiment. Verification of MM5 forecasts against satellite and radiosonde data reveals a strong cloudy bias in the mid- to upper troposphere, significant moist biases aloft and near the surface, and a deep cold bias through much of the troposphere. The cloudy bias and upper-level moist bias are traced to an inappropriate assumption in the microphysical parameterization. Simple changes to the parameterization greatly improve the cloud forecast. A portion of the deep cold bias is attributed to the simple parameterization of atmospheric radiation used for the forecasts. The low-level cold and moist biases are in large part due to the climatological values of soil moisture availability as a function of land-use category. ...
COMPARATIVE ACYL SPECIFICITIES FOR TRANSFER AND SELECTIVE UPTAKE OF HIGH DENSITY LIPOPROTEIN CHOLESTERYL ESTERS

This study compares the specificities of selective uptake and transfer mediated by plasma cholesteryl ester transfer protein (CETP) for various species of cholesteryl esters in high density lipoproteins (HDL). [3H]Cholesterol was esterified with a series of variable chain length saturated acids and a series of variably unsaturated 18-carbon acids. These were incorporated into synthetic HDL particles along with 125I-labeled apoA-I as a tracer of HDL particles and [14C]cholesteryl oleate as an internal standard for normalization between preparations. Selective uptake by Y1-BS1 mouse adrenal cortical tumor cells was most extensively studied, but uptake by human HepG2 hepatoma cells and fibroblasts of human, rat, and rabbit origin were also examined. Acyl chain specificities for selective uptake and for CETP-mediated transfer were conversely related; selective uptake by all cell types decreased with increasing acyl chain length and increased with the extent of unsaturation of C18 chains. In contrast, CETP-mediated transfer increased with acyl chain length, and decreased with unsaturation of C18 chains. The specificities of human and rabbit CETP were also compared, and were found to differ little. Associated experiments showed that HDL-associated triglycerides, traced by [3H]glyceryl trioleyl ether, were selectively taken up but at a lesser rate than cholesteryl esters. The mechanism of this uptake appears to be the same as for selective uptake of cholesteryl esters.
Density dependence and its impact on individual growth rates in an age‐structured stream salmonid population

In organisms with flexible and indeterminate growth, demographic density dependence can affect both individual fitness and population dynamics. Recent work in stream salmonids suggests that individual growth rates can be depressed even at low population densities, which warrants examination of populations previously assumed to be below carrying capacity. We investigated the effects of population density on individual growth rates in a threatened population of steelhead (Oncorhynchus mykiss) in a tributary to the Clearwater River in Idaho, USA. We followed a mark-recapture design where we visited 16 study sites on average five times per year from 2010 to 2012. The 95% confidence interval for average growth rates (% change in body mass per day) for subyearlings were [0.82, 1.0]) and [0.16, 0.30] for yearling steelhead. Variance decomposition showed that the variation in growth rates could be attributed equally to individual- and visit-level factors in subyearlings, whereas almost two-thirds of the variance in yearling growth rates could be attributed to individual-level factors. Growth rates in the subyearling age class were negatively related to the densities of yearling steelhead, but not vice versa. Yearling growth rates showed no evidence of density dependence. Finally, density in interaction with water temperature did not affect growth rates of either age class. Our results demonstrate that density dependence can pose constraints on individual growth rates at low population densities (<1 fish m−2) in stream salmonids, and underscore the importance of considering age classes separately when studying density dependence in age-structured populations.
Ecological Niche Modeling Using the Kepler Workflow System

Changes in biodiversity have been linked to variations in climate and human activities [295]. These changes have implications for a wide range of socially relevant processes, including the spread of infectious disease, invasive species dynamics, and vegetation productivity [27, 70, 203, 291, 294, 376, 426]. Our understanding of biodiversity patterns and processes through space and time, scaling from genes to continents, is limited by our ability to analyze and synthesize multidimensional data effectively from sources as wide-ranging as field and laboratory experiments, satellite imagery, and simulation models.
Design procedures and NML cost analysis of reversible barrel shifters optimizing garbage and ancilla lines

Reversible computing generates a unique output from each input and vice versa. In addition, conservative reversible logic is useful to design ultra-low-power nanocomputing circuits, circuits for quantum computing, and nanocircuits that are testable in nature. Reversible computing circuits require ancilla inputs and garbage outputs to maintain reversibility. An ancilla input is the constant input in a reversible circuit. A garbage output is an output which exists in the circuit just to maintain one-to-one mapping but is not a primary nor a useful output. An efficient reversible circuit will have a minimal number of garbage and ancilla bits. Furthermore, the barrel shifter is one of the main computing systems having applications in high-speed digital signal processing, floating-point arithmetic, field programmable gate arrays, and central processing units. A barrel shifter can shift and rotate multiple bits in a single clock cycle. In this work, we proposed five designs of barrel shifters based on reversible computing that are optimized in terms of the number of garbage outputs and the number of ancilla inputs. To achieve this goal, a new super conservative reversible logic gate (SCRL gate) has been proposed. The SCRL gate has 1 control input depending on the value of which it can swap any two $$n-1$$n-1 data inputs. The five proposed designs consist of reversible right rotator, reversible logical right shifter, reversible arithmetic right shifter, reversible universal right shifter, and reversible universal bidirectional shifter. The proposed designs of reversible barrel shifters are compared with the existing works in the literature and have shown improvements ranging from 8.57 to 91.62 % in terms of the number of ancilla inputs and from 17.72 to 91.62 % in terms of the number of garbage outputs. A cost analysis was made for their potential implementation in nanomagnetic logic (NML) computing. It is illustrated that the SCRL gate-based designs of reversible barrel shifters have less NML cost (cost in terms of number of inverters and majority voters) compared to the Fredkin gate-based designs of reversible barrel shifters.
Necropolitical voices and bodies in the rhetorical reception of Iranian women's asylum claims

ABSTRACTIn the mid-1990s, US immigration courts were introduced to a group of Iranian women who claimed that they feared persecution because of their “pro-Western and feminist” political opinions and because of the way they performed gender on their bodies. The claims were, in total, unsuccessful bids to asylum. Analyzing these cases set against the geopolitical background of US–Iranian history and contemporary relations, I argue that their denials illustrate three important dynamics. First, building on rhetorical theorizing of voice and body, this essay demonstrates the uneasy reception in US law and politics of willful noncitizen women of color with explicit political voices and bodies, and second, the consequential racialization of these subjects as willful, unorderable migrant subjects too akin in their sovereignty to their state of birth. Third, this analysis adds to the field's attentiveness to geopolitics by consequently demonstrating US necropolitical desires toward Iran in the state's engagement ...
FURTHER EVIDENCE ON SEXUAL ISOLATION WITHIN DROSOPHILA ATHABASCA.

As is well known, the genus Drosophila contains certain species divided within themselves into reproductively isolated, genetically divergent subdivisions-e.g., as discussed by Dobzhansky (1963), who reviews the status of the well studied Drosophila paulistorum and D. serrata (more recently reported on by Dobzhansky et al., 1964, and Ayala, 1965, respectively). It may reasonably be expected that more such cases remain to be discovered in Drosophila. In this paper we present additional evidence that the widely distributed North American species Drosophila athabasca is divided by sexual isolation. The existence of sexual isolation within D. athabasca was reported by Miller (1958a), who encountered a fairly strong three-way sexual isolation between laboratory strains of this species from Wyoming, Michigan, and New York. Although no reliable morphological traits were found to distinguish the populations from which these stocks were derived, the western strains (Wyoming, etc.) differed from the eastern ones in a behavioral trait, duration of copulation, those from the west having long copulation times (4 minutes or more), those from the east short copulation times (less than 2 minutes). Later it was demonstrated that stocks of D. athabasca varied as to Y chromosome morphology (Miller, 1958b; Miller and Stone, 1962; Miller and Roy, 1964). Western and northern strains have been found usually to have a large J-shaped Type I Y chromosome, while those of the east and southeast have
December 2, 1942: the event and the people

(1982). December 2, 1942: the event and the people. Bulletin of the Atomic Scientists: Vol. 38, No. 10, pp. 22-32.
The duty to care--the right to refuse. Changing roles of patients and physicians in end-of-life decision making.

(1998). The duty to care—The right to refuse. Journal of Legal Medicine: Vol. 19, No. 1, pp. 99-125.
Response to Robert Jackson

In my view, historians have long given scant notice to the topics of health care and disease, matters that actually deserve muclh attention. Robert Jackson rightly calls for a fuller understanding of the causes and responses to health conditions and has highlliglted several themes, especially poverty and underdevelopment, for miore discussion. I welcome the opportunity to further open up this topic, first by offering some additional observations on the case of Guayaquil, and second by sketching a few hypotheses for consideration as we take up the study of comparative healtlh conditions in other Latin American cities. As Jackson points out, even before the development of a modern scientific understanding of the origin and spread of disease, some public healtlh care measures were still effective. Quarantining and vaccination, he correctly notes, proved fairly successful in combating illnesses like bubonic plague and smallpox. In Guayaquil, as elsewhere, the prevailing notion that disease stemmed from evil, putrid airs-miasmas-led officials to call for cleanup campaigns to rid the city of the sources of these foul winds. Obviously such measures could be beneficial. Draining pools of water shrank mosquitobreeding areas, thereby reducing the risk of malaria and yellow fever. Hauling away human waste, offal, and garbage reduced the chan-ce that drinking water and food would be contaminated, thereby lowerinig the threat from enteric disorders, cholera, and typhoid fever. Cleaning and disinfecting living quarters reduced the riisk of tuberculosis, and controlling the flea population in dwellings helped lower the threat from bubonic plague and typhus.
Analysis of the Basic Issues of the Personality Trait Theory

Trait theory is a relatively early paradigm to analyze personality.With the tide of fivefactor model research,it has become the research focus of personality psychology.The author summarizes those criticisms and opinions the theory has suffered or is suffering,and discusses its basic issues,such as suspicion about circulation argument,correlation of trait and behavior,rationality of assumption of language and applicability of factor analysis,conflict and balance between generic approach and idiographic approach in research and the issue of valuefree.
Uncertainty Evaluation on the Field Measurement Result of Carbon Monoxide Concentration in the Air of Workplaces

[Objective] To study the uncertainty evaluation method for the field measurement result of carbon monoxide concentration in the air of workplaces and the application of the uncertainty results.[Methods]The methods of national standard GBZ/T 160.28-2004 and JJF 1059-1999 were adopted to build a mathematical model of field measurement of carbon monoxide concentration in the air of workplaces. The uncertainty components and variances of the field measurement result of carbon monoxide concentration in the air of the boiler room of a beverage company were calculated.[Results]The expended uncertainty was U=0.17 mg/m3, Ueff=6, P=95%, and the carbon monoxide concentration was (1.4±0.17) mg/m3.[Conclusion]The result of carbon monoxide concentration of the boiler room accorded with GBZ/T 2.1-2007. And the method could be applied as reference on the uncertainty evaluation of field measurement result of some detection parameters, such as carbon monoxide concentration in the air of workplaces.
A New Exploration into the Cultivation Mode of Innovative Graduates

The innovative mode of education should come first in the field of education.Taking the advantage of the opportunity of Graduate Education Innovation Project" and centering around the students,the limitless potential innovativeness of the students can be highlighted;starting with the help of the state-sponsored projects to enhance the self-construction will help the sustainable development;not focusing on the experiment results but emphasizing the cultivation of innovative ability in practice is good for exploring the new cultivation mode of innovative graduates.
HIV and the cells it infects: sorting the latent from the labile. An interview with Mike McCune, MD, PhD. Interview by Mark Mascolini.

AIDS: Dr. Mike McCune, a research scientist specializing in HIV research and AIDS, discusses a variety of research topics, including viral genetics and immunology. In the interview, McCune considers whether destruction of cells by HIV is a direct or indirect action. McCune studies effective drug combinations, cytokine-based and gene therapies, and information from animal disease models.
Treatment of aplastic anemia by bone marrow transplantation in identical twins

Abstract Four patients with aplastic anemia were treated with intravenous infusion of 0.8-3.5 × 108 nucleated bone marrow cells/kg obtained from their healthy identical twin. In two cases, simple marrow infusion led to prompt recovery of bone marrow function. In the other two cases, bone marrow infusion alone was ineffective, but a second infusion after treatment with cyclophosphamide (CY) led to prompt complete recovery. Coculture studies using patients' peripheral blood mononuclear cells and donor bone marrow or peripheral blood cells were performed for three of the patients prior to bone marrow transplantation. Cells from the two patients who ultimately required CY appeared to inhibit granulocytic or erythroid colony growth by donor marrow, whereas cells from the one patient who was studied who responded to marrow infusion alone did not. The response of patient peripheral leukocytes to twin cells in mixed leukocyte culture was compared to the response of patient cells to a cell pool from unrelated donors and expressed as a relative response. The response was abnormally high in the two cases requiring CY and normal in the other two cases. The results suggest that aplastic anemia in some cases reflects a qualitative or quantitative marrow cell defect correctable by the simple infusion of twin marrow, but in other cases reflects active suppression of hematopoiesis that can be overcome by CY and bone marrow transplantation.
Recent Developments in Y-Short Tandem Repeat and Y-Single Nucleotide Polymorphism Analysis.

This article reviews new genetic markers on the Y-chromosome and methods for analyzing these short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci. Relative chromosomal locations for over 50 Y-chromosome STRs (Y-STRs) are described along with their repeat motif and allele range characteristics based on published population studies. Multiplex assays for typing many of these markers in a parallel fashion are discussed, as are newly available commercial Y-STR kits. Approximately 250 SNP markers are now catalogued along the Y-chromosome (Y-SNPs) with a unified haplogroup nomenclature describing their relative relationships. Technologies for typing these Y-SNPs are reviewed including primer extension and allele-specific hybridization methods. Finally, available reference materials for standardization of allele calls, Y-STR allele nomenclature issues, and published validation and interlaboratory studies are reviewed.
The Nature of Prostate Cancer Detected Through Prostate Specific Antigen Based Screening

AbstractProstate specific antigen (PSA) based screening nearly doubles the detection rate of early prostate cancer. However, it is unknown whether the additional tumors detected are medically important. Traditional clinical and pathological features associated with medically important cancer include a palpable tumor, multifocal or diffuse involvement and moderately or poorly differentiated histology. In contrast, microfocal, well differentiated tumors are considered to be possibly medically unimportant.We sought to examine the clinical and pathological tumor stage and tumor grade in 1,169 consecutive men whose prostate cancer was detected during serial PSA based screening protocols involving 24,346 men screened at 6-month intervals. Of the patients 97% had clinically localized (clinical stage T1 or T2) tumors, of which 39% were not palpable (stage T1). Of the men whose cancer was detected through initial screening who underwent surgical staging 69% had pathologically organ confined (pathological stage who...
Coleridge and Alcohol: Songs and Centrifuges

Coleridge’s position as an example of the double experience of drunkenness for medical commentators; as the veiled substitute figure behind Wordsworth’s examination of Burns; as a companion, witness and interlocutor of Lamb’s giddy instabilities; and as the formative father of a notably enfeebled drunkard puts him at the centre of a Romantic network of writings about drink. His own writings on the subject take jocular, confessional, philosophical, sociological and aesthetic forms.
Optimized procedure for sol–gel production of La2/3Ca1/3MnO3 thin films

Lanthanum calcium manganese oxide $$\left( \hbox {La}_{(1-x)} \hbox {Ca}_x\hbox {MnO}_3\right)$$ has a number of potentially useful magnetic and electrical properties that can be adjusted based upon its calcium fraction, x. This material has been fabricated in a number of ways, but as we approach a point at which it can be used in complex commercial applications, it is critical that we consider the cost of generating thin films in complex geometries. Therefore, we present an optimized sol–gel synthesis and thin-film generation procedure that results in repeatable, high-quality thin films of a specified thickness.
The Financial Front

Probably no industry is more strategic than that which peddles cash, stocks, bonds, and other money-making schemes. All other industries depend on finance for their investments in research and development, production and marketing. Where they obtain the finance, how much, and at what terms is a vital factor in that industry’s future. Money-lenders in turn obtain intimate understandings of a firm’s operations, strategy and strengths and weaknesses. Those nations which achieve the most virtuous savings/investment cycles enjoy the most dynamic economies, greatest wealth, and accompanying power. The most potentially powerful nation in an interdependent world is the largest lender. The power to grant or deny loans to foreign governments or corporations, or set the terms at which loans are granted is the power to shape other nations’ economic destinies. Likewise, the weaker a state’s financial system, the weaker its entire economy and the more dependent it is on global bankers to finance development. Thus virtually all countries carefully regulate their financial sectors to prevent bankruptcy or foreign control, and to achieve virtuous savings/investment cycles. The means by which nations achieve these ends vary considerably from one nation to the next. Some nations like Japan have been extremely successful in creating powerful financial and industrial systems that minimize their dependence on foreign credit; other nations like the United States have followed disastrous policies which produce chronically weak financial and industrial systems which have left it addicted to foreign capital.
The Blueshirt Episode and its Background

It is well known that Yeats was associated for a time with the Blueshirts, an Irish political movement which was at least superficially fascist, and which Yeats believed was fundamentally fascist. There are good reasons for not considering this episode especially significant. First, it was contemporaneous with other extravagant episodes — the Steinach operation, the collaboration with Shri Purohit Swami, the sponsorship of Margot Ruddock — the meaning of which seems to lie in their very extravagance, in their keeping with Yeats’s wish, expressed in a poem of the time, to avoid ‘all that makes a wise old man’ that he might seem a ‘foolish, passionate man’.1 Second, the episode lasted less than a year, and Yeats ended by publicly dissociating himself from the movement. Third, the Blueshirts themselves enjoyed only a ‘brief period of vigour’, according to one of their founders,2 their main accomplishment being their ‘adding colour to the drabness of life in the 1930s’, as historian John Murphy has wittily noted.3 Since, however, Yeats was perhaps the greatest poet of his time, and fascism perhaps the most potent political force between the wars, so potent as to loom in our arguments and nightmares down to the present day, the episode is bound to interest us and provoke us to speculation.
Information Literacy: A Theological Librarian Reflects on Writers and Writing

Consider first what research-based writing is not. It is not creative writing, although creative writers will often research some aspect of their subject. It is not journalistic writing, although the journalist makes steady use of sources. It is not writing for publication, since it seldom finds an audience of more than five. It is not an essay, although it has a beginning, middle, and end. Certainly, it is rarely a sermon, even though the preacher has been taught to build the sermon around one central idea.1 Eliminating these options, what remains?
Esophagogastric Junction Morphology and Distal Esophageal Acid Exposure.

The Chicago classification has recently added a morphological subclassification for the esophagogastric junction (EGJ). Our aim was to assess the distal esophageal acid exposure in patients with this new Chicago EGJ-type IIIa and IIIb classification. From a prospectively collected high-resolution manometry (HRM) database, we identified patients who underwent 24-h pH study between October 2011 and June 2015 and were diagnosed with EGJ-type III based on HRM. Chicago EGJ-type III is defined as the inter-peak nadir pressure ≤gastric pressure and a lower esophageal sphincter (LES)–crural diaphragm (CD) separation >2 cm [IIIa-pressure inversion point (PIP) remains at CD level and IIIb-PIP remains at LES level]. We classified the patients into reflux group [DeMeester score >14.72 or Fraction time pH ( 4.2 %] and non-reflux group based on 24-h pH study. Fifty patients were identified that satisfied the study criteria, of which 37 patients (74 %) were EGJ-type IIIa. In those with EGJ-type IIIb, abdominal LES length (AL) in reflux group was significantly shorter than the non-reflux group (0.8 vs. 1.8, p 2-cm LES–CD separation (type IIIb) maintain a physiological intra-abdominal location of the EGJ and are less likely to have reflux. A LES–CD ≥ 3 cm seems to discern a hiatus hernia of clinical significance.
Estimation and monitoring of key performance indicators of manufacturing systems using the multi-output Gaussian process

Recently, the estimation and monitoring of manufacturing key performance indicators (KPIs) have drawn significant attention. In this article, a KPI estimation and monitoring method using a multi-output Gaussian process (MGP) is proposed. The Gaussian process (GP) is an effective non-parametric flexible tool for data-driven statistical modelling for various systems. The unique features of the proposed method is that the MGP enjoys the high flexibility and desirable analytical properties of the GP while also capturing the correlation between different KPIs, thus providing better estimation accuracy and error quantification. The advantageous features of the proposed method are demonstrated through a numerical study as well as a case study with real world data in the estimation and monitoring of throughput for a multiclass production operation.
Autoantibodies in Sera from Patients with L-Tryptophan-Associated Eosinophilia-Myalgia Syndrome: Demonstration of Unique Antigen-Antibody Specificities

The purpose of this study was to determine whether specific autoantibodies could be identified that are associated with eosinophilia-myalgia syndrome (EMS). Sera from 44 patients with EMS were tested by indirect immunofluorescence, immunodiffusion against calf thymus extract, and immunoprecipitation from HeLa cell extract. Antinuclear antibodies were detected in the sera of 24/39 patients with EMS (61.5%) by indirect immunofluorescence against HEp-2 cells. Seven patients (16%) were demonstrated to have specific autoantibodies by immunoprecipitation in which at least two shared patterns were noted. In three sera immunoprecipitation identified a similar 63-kDa band (Ab-1). An additional four sera shared a pattern of bands consisting of a strong 110-kDa protein and a weak 95-kDa protein (Ab-2). Absorption of HeLa extract with a strongly positive Ab-2 serum confirmed that the four patients shared the same antibody. In conclusion, the detection of these autoantibodies provides evidence of autoimmunity in EMS, and may distinguish this syndrome from clinically related conditions.
Splenic Enlargement and Bone Marrow Hyperplasia in Patients Receiving Trastuzumab-Emtansine for Metastatic Breast Cancer

An association between trastuzumab-emtansine (T-DM1) and splenic enlargement is reported in preclinical data, and has been noted anecdotally in patients receiving T-DM1 at our institution. Use of whole-body MRI examinations (WB-MRI) allows for detailed bone marrow assessment and semi-automated splenic volume calculations. To retrospectively evaluate changes in splenic volume versus evidence of bone marrow hyperplasia and/or changes in portal venous pressure in patients receiving T-DM1 for metastatic breast cancer. Twelve metastatic breast cancer patients underwent 29 WB-MRIs before and during T-DM1 therapy. Splenic volume, portal vein diameter, bone marrow diffusion-weighted normalised signal intensity (nSI), quantitative water diffusivity (apparent diffusion coefficient, ADC) and fat fraction (rF%) were measured and correlated. Splenic volume increases were observed in 92% of patients. Mean splenic volume increased from 144 cm3 (95% CI 110–177 cm3) to 209 cm3 (95% CI 161–257 cm3) on T-DM1 therapy (p = 0.006). Splenic volume increases correlated with treatment duration (r2 = 0.43). Bone marrow hyperplasia was evidenced by an increase in bone marrow nSI (3.5 to 4.8, p = 0.12), and decreases in rF% (64.3% to 57.3%, p = 0.12) and ADC (655 μm2/s to 543 μm2/s, p = 0.11). No changes to portal vein diameter were seen. Previously unreported increases in splenic volume and bone marrow hyperplasia are observed on WB-MRI in patients on T-DM1 therapy. Caution must be applied to avoid misinterpreting T-DM1-induced bone marrow hyperplasia as diffuse disease progression in bone.
Il ruolo sociale della biblioteca digitale

L’articolo indaga il valore sociale delle biblioteche digitali. Inizia esplorando le concezioni passate e presenti del valore delle biblioteche per le loro comunita. Prendendo come punto di partenza la cornice concettuale ben nota che delinea il ruolo sociale delle biblioteche, l’articolo propone un possibile nuovo quadro concettuale per descrivere quello delle biblioteche digitali. Il resto dell’articolo descrive questo potenziale ruolo sociale delle biblioteche digitali, esplorandone i singoli aspetti. Ricorrendo ad esempi specifici, il testo prende in considerazione benefici e sfide e fa riferimento a letture chiave di studiosi e professionisti della biblioteca digitale.
Radiotherapy alone or combined with chemotherapy for base of tongue squamous cell carcinoma.

Objectives/hypothesis To evaluate the long-term disease control, survival, and complications after definitive radiotherapy (RT) alone or combined with adjuvant chemotherapy with or without planned neck dissection for base of tongue squamous cell carcinoma (SCC). Study design We retrospectively reviewed the medical records of 467 patients treated at the University of Florida with definitive RT alone or combined with adjuvant chemotherapy between 1964 and 2011 for base of tongue SCC. Methods Median follow-up was 5.6 years. Median total dose to the primary site was 74.4 Gy. Eighty-seven patients (19%) were treated with once-daily fractionation, and 380 (81%) received altered fractionation schedules. Intensity-modulated RT was used in 128 patients (27%). Chemotherapy was administered to 173 (37%) patients. Planned neck dissection after RT was performed in 226 patients (48%). Data regarding p16 pathway activation were available for 25 patients. Results At 5 years, the local, local-regional, and regional control rates were 85.5%, 80.0%, and 90.0%, respectively. The 5-year overall, cause-specific, and distant metastasis-free survival rates were 59.1%, 71.5%, and 84.1%, respectively. Sixty-four patients (14%) developed one or more severe late complications. Fifty patients (11%) required late gastrostomy tube placement. Conclusions This study supports the continued use of RT alone or combined with adjuvant chemotherapy for patients with base of tongue SCC, as this treatment yields high rates of cause-specific survival and disease control, with a relatively low rate of late complications. Level of evidence 4. Laryngoscope, 127:1589-1594, 2017.
Clinical and analytical performance of non-small cell lung cancer biomarkers.

11070 Background: A variety of biomarkers are currently used to help guide treatment decisions for patients with non-small cell lung cancer (NSCLC). These include mutation analysis for the EGFR and KRAS genes, along with gene rearrangement analysis for the ALK and ROS1 loci. In this study we have evaluated the clinical and analytical performance features of these assays in a series of formalin-fixed paraffin-embedded (FFPE) tissue samples. Methods: FFPE samples submitted for analysis of the EGFR, KRAS, ALK and ROS1 genes were evaluated using molecular and FISH assays. EGFR mutation analysis was performed using Sanger nucleic acid sequencing methods for exons 18-21. KRAS mutations were detected using allele specific PCR or pyrosequencing methods. Rearrangements involving the ALK gene were detected using break-apart FISH probes (Abbott Molecular). Genetic alterations involving the ROS1 gene were determined using FISH probes (Kreatech Diagnostics). Over 6,200 test results for these 4 markers are included in ...
Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices

Adult tissue stem cells (SCs) reside in niches, which, through intercellular contacts and signaling, influence SC behavior. Once activated, SCs typically give rise to short-lived transit-amplifying cells (TACs), which then progress to differentiate into their lineages. Here, using single-cell RNA-seq, we unearth unexpected heterogeneity among SCs and TACs of hair follicles. We trace the roots of this heterogeneity to micro-niches along epithelial-mesenchymal interfaces, where progenitors display molecular signatures reflective of spatially distinct local signals and intercellular interactions. Using lineage tracing, temporal single-cell analyses, and chromatin landscaping, we show that SC plasticity becomes restricted in a sequentially and spatially choreographed program, culminating in seven spatially arranged unilineage progenitors within TACs of mature follicles. By compartmentalizing SCs into micro-niches, tissues gain precise control over morphogenesis and regeneration: some progenitors specify lineages immediately, whereas others retain potency, preserving self-renewing features established early while progressively restricting lineages as they experience dynamic changes in microenvironment.
PREPARING AN ACCOUNTING PROFESSIONAL: THE ARTICLES OF CLERKSHIP (1892–1897) OF GEORGE OLIVER MAY

George O. May, one of, if not ‘the’ leading spokesman for the American Institute of CPAs for most of his lifetime, was the product of British education and an articled clerkship. This paper reviews...