cssi/SciSciGPT-SciSciNet huggingface dataset:
BatchPrimer3: A high throughput web application for PCR and sequencing primer design

Microsatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded. A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories. BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/ .
Selective Inhibition of Muscle Gene Expression by Oxidative Stress in Cardiac Cells

Reactive oxygen species have been suggested to play an important role in damage to cardiac tissue following ischemia and reperfusion. Oxygen radicals may also contribute to the cardiotoxicity of the anthracycline antibiotics, such as doxorubicin. We tested whether a selective inhibition of muscle gene expression, previously observed in cardiocytes treated with doxorubicin, might be reflective of a more generalized response evoked by oxidative stress in cardiac tissue. Cardiocytes in culture were exposed to hydrogen peroxide or glucose oxidase, and the effects on muscle gene expression were measured. Exposure to these agents led to a reduction in the levels of mRNA for the muscle-specific genes cardiac alpha-actin, troponin I, myosin light chain 2 (slow), and M isoform of creatine kinase, without affecting levels of the non-muscle genes pyruvate kinase and beta-actin. The magnitude of this effect was similar to that observed with doxorubicin. Although the hydrogen peroxide scavenging enzyme catalase and the intracellular radical scavengers N-acetylcysteine and 1,3-dimethyl-2-thiourea were without effect on doxorubicin-dependent reduction in gene expression, they inhibited the reduction in muscle gene expression mediated by hydrogen peroxide. These observations suggest that oxygen free radicals modulate muscle gene expression in cardiocytes by a pathway distinct from that utilized by doxorubicin.
Multiview image coding using local orthogonal bases

Source coding of multi-view image sequences is investigated. Two different frameworks are considered. The first one is a bidirectional predictive coding scheme, in which the displayed frames can be instantaneously decoded given the coded furthest right and left images. The second one is a unidirectional predictive coding scheme, in which the central frame is an I-frame and the remaining frames are coded based on this frame. Both frameworks can overcome problems related to occlusion, are compatible with current and proposed image and video coding standards, consider the special indexing characteristics of multi-view sequences, and can be implemented in applications where the display device has a small buffer. The actual coding is performed using the subspace projection technique, a locally adaptive transform approach. The transformation matrix is equivalent to a projection operation and is determined using the local cross-correlation characteristics. Several design issues in generating the adaptive transforms and experimental results are presented.© (1997) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Beyond Eve and Mary: Filipino American Intellectual Heroes and the Transnational Performance of Gender and Reciprocity

In a 2002 article for the San Francisco–based periodical Asian Week, columnist Emil Guillermo revealed that the Federal Bureau of Investigation (FBI) had indeed spied upon the Filipino American aut...
American Modern Dance: Primary Sources in Book Form at the University of Michigan Music Library

Conventional wisdom holds that the art of dance is strictly and in all its aspects a phenomenon of the moment, something adequately captured by pictorial means only, and not by the written word. Reading and writing are thought to have little or nothing to do with the ephemeral magic of the art of dance. This attitude has its roots in a time before film and video technologies made more possible the vivid preservation of choreography; it also has its roots in a time before the importance of preserving our unique modern dance heritage became fully evident.
Defining and measuring patient satisfaction with medical care

Abstract This paper describes the development of Form II of the Patient Satisfaction Questionnaire (PSQ), a self-administered survey instrument designed for use in general population studies. The PSQ contains 55 Likert-type items that measure attitudes toward the more salient characteristics of doctors and medical care services (technical and interpersonal skills of providers, waiting time for appointments, office waits, emergency care, costs of care, insurance coverage, availability of hospitals, and other resources) and satisfaction with care in general. Scales are balanced to control for acquiescent response set. Scoring rules for 18 multi-item subscales and eight global scales were standardized following replication of item analyses in four field tests. Internal-consistency and test-retest estimates indicate satisfactory reliability for studies involving group comparisons. The PSQ well represents the content of characteristics of providers and services described most often in the literature and in response to openended questions. Empirical tests of validity have also produced generally favorable results.
Modeling of strengthening mechanisms in irradiated fusion reactor first wall alloys

Abstract Tensile property evaluations of austenitic stainless steels irradiated at 60 to 400°C in the ORR have been conducted. The neutron spectrum was tailored to achieve the appropriate helium/dpa ratio for austenitic stainless steels in a fusion reactor. The components of the alloy microstructure considered to contribute to strengthening are black dot defect clusters, Frank loops, network dislocations, voids, bubbles, and precipitates. Accepted expressions for hardening by defect interactions were employed in the calculation. It was found that the strengthening could be accounted for by the observed defects at temperatures below 330°C. However, strength was underpredicted at the higher temperatures. Since the voids and precipitates were observed to nearly always occur in coupled pairs, they were considered to be one large defect contributing to hardening through the Orowan bowing mechanism. This mechanism alone could not account for the strengthening observed. However, radiation-induced segregation of alloy components to the bubbles could account for the observed hardening, although defects below the limit of detectability are also believed to make a contribution.
Inactivation of Ichthyophonus spores using sodium hypochlorite and polyvinyl pyrrolidone iodine

Chlorine and iodine solutions were effective at inactivating Ichthyophonus spores in vitro. Inactivation in sea water increased directly with halogen concentration and exposure duration, with significant differences (P < 0.05) from controls occurring at all chlorine concentrations and exposure durations tested (1.5-13.3 ppm for 1-60 min) and at most iodine concentrations and exposure durations tested (1.2 ppm for 60 min and 5.9-10.7 ppm for 1-60 min). However, 10-fold reductions in spore viability occurred only after exposure to halogen solutions at higher concentrations and/or longer durations (13 ppm total chlorine for 1-60 min, 5.9 ppm total iodine for 60 min, and 10.7 ppm total iodine for 1-60 min). Inactivation efficacy was greater when halogen solutions were prepared in fresh water, presumably because of combined effects of halogen-induced inactivation and general spore instability in fresh water. The results have practical implications for disinfection and biocontainment in research laboratories and other facilities that handle live Ichthyophonus cultures and/or infected fish.
Identification and characterization of developmentally regulated mRNP proteins of Dictyostelium discoideum.

Abstract The isolation of poly(A) + polysomal and nonpolysomal RNPs by oligo(dT)-cellulose chromatography has led to the identification of more than 20 polypeptides that bind to the poly(A) + mRNA in growing Dictyostelium cells. Most of these polypeptides were identified in experiments using short-wave UV light (254 nm) to crosslink specifically bound proteins to the RNA. Digestion of the RNPs with ribonucleases A and T 1 prior to their application to oligo(dT)-cellulose permitted the isolation of the 3′ poly(A)-protein complexes. In polysomal RNPs, two major polypeptides, with molecular weights of 31,000 (p31) and 31,500 (p31.5), are bound to poly(A). These proteins can also be purified from cytoplasmic extracts by affinity chromatography on poly(A)-Sepharose. Partial proteolytic digestion of p31 and p31.5 indicates that they are closely related. The UV-crosslinking experiments established that p31 and p31.5 bind to the non-poly(A) segments of mRNA as well. In nonpolysomal RNPs, p31 and a polypeptide with a molecular weight of 29,500 (p29.5) are the major species associated with poly(A). Partial proteolytic digestion of p29.5 indicates that it is closely related to p31 and p31.5. Only small amounts of p29.5 were observed in the polysomal poly(A)-protein complexes. Early in Dictyostelium development, when cellular translation activity is sharply reduced, most of the p29.5, p31 and p31.5 present is selectively degraded. These observations are consistent with a translational role for these proteins.
Metabolism of Androgens by Human Periodontal Ligament

The metabolism of androgens (testosterone and androstenedione) has been studied in healthy and diseased human periodontal ligaments. An increased activity of 17β-oxidoreductase and 17-keto-5α-A-ring reductase and decreased activity of 17β-hydroxy-5α-A-ring reductase, 3αβ-oxidoreductase and 5β-A-ring reductase have been found in diseased periodontal ligament.
Gene expression profiling of wound healing in keratinocytes using DNA microarrays

Wound repair is a complex biological process involving cell migration, proliferation and differentiation of multiple cell types. A number of growth factors, receptors, matrix molecules and proteases have been shown to be important during wound healing. However, a detailed knowledge of the underlying gene expression changes occurring during wound healing would further improve our understanding of the repair process and how this may be disrupted in diseases of reduced or excessive wound healing.
An Interview with Edward J. Valauskas

In May 2003 Heather Cannon interviewed Edward J. Valauskas, manager of the Library and Plant Information Office of the Chicago Botanic Garden and chief editor of First Monday. Valauskas discusses the issues surrounding producing e-journals, as well as the skills librarians will need to work with changing technologies in the future. Valauskas also describes the Chicago Botanic Garden's recent acquisition of a collection of rare historical books and journals about botany and horticulture from the Massachusetts Horticultural Society. Serials Review 2003; 29:305–310.
Photoperiodic Entrainment Patterns in the CO2 Output of Lemna perpusilla 6746 and of Several Other Lemnaceae

The CO 2 output of Lemna perpusilla 6746 in “skeleton photoperiods” consisting of alternating 10½-hour and 13-hour dark periods separated by ¼-hour illuminations was recorded under stable high and low nitrate conditions. The phase relationship finally attained between light schedule and output is the same regardless of which dark period is given first, but entrainment is more rapid (as is flowering) with an initial 13-hour dark period. In all respects other than bistability—the assumption of two different stable phase relationships depending on the initial dark period—both flowering and the course of CO 2 output conform to Pittendrigh9s model derived from Drosophila eclosion rhythms, confirming the view that an endogenous circadian rhythm, or biological clock, underlies the photoperiodic control of flowering in this plant. Experiments with rigorous temperature control show that earlier results with long light exposures were in part due to temperature changes; in consequence, it is clear that entrainment patterns with high nitrate differ even more from those in low nitrate than was previously evident, and not simply by the addition of a “nitrate peak.” Other Lemnaceae tested with a few simple light-dark schedules in both types of media show a variety of responses, with no obvious correlation to photoperiodic response type.
In situ TEM study of crack–grain boundary interactions in thin copper foils

In situ tensile experiments were performed in a transmission electron microscope to investigate the interaction of an advancing crack with grain boundaries in thin copper foils. Cracks propagate within the grains on slip planes due to plastic flow, thinning and overload. Certain grain boundaries are effective in arresting the crack whereas others are not. The stress field of the arrested crack then activates multiple deformation modes in the grain ahead of the crack tip. The observations have significant implications for grain boundary engineering in polycrystalline metal films.
Lower CSF Homovanillic Acid Levels in Depressed Patients with a History of Alcoholism

Major depression and alcoholism are often comorbid, resulting in more impairment and more suicidal behavior compared with either diagnosis alone. This study compared clinical features and cerebrospinal fluid (CSF) monoamine metabolites in depressed subjects with and without a history of alcoholism and healthy volunteers. We hypothesized that depressed subjects with a history of alcoholism would be more aggressive, impulsive, and suicidal than depressed subjects without a history of alcoholism, and would have lower CSF monoamine metabolite levels. We compared 63 subjects with a current major depressive episode (MDE) and a history of alcoholism, 72 subjects with a current MDE but without a history of alcoholism, and 22 healthy volunteers. Participants with a history of alcoholism were in remission for at least 6 months. All subjects were free from prescribed medications known to affect brain serotonin, dopamine, or norepinephrine systems for a minimum of 14 days. Depressive symptoms, lifetime aggression, impulsivity, Axis II disorders, and suicidal behavior were assessed. CSF was sampled and homovanillic acid (HVA), 5-hydroxyindolacetic acid (5-HIAA), and 3-methoxy-4-hydroxyphenylglycol (MHPG) were assayed by high-performance lipid chromatography with electrochemical detection. Depressed subjects with a history of alcoholism did not differ from depressed subjects without a history of alcoholism in current severity of depressive symptoms, or in past suicidal behavior. Depressed subjects with a history of alcoholism had lower CSF HVA levels, and higher lifetime aggression and current suicide ideation scale scores and were more likely to be tobacco smokers compared with depressed subjects without a history of alcoholism. Low HVA was present after adjustment for sex, aggression and depression scores, cigarette smoking, antisocial and borderline personality disorders, psychomotor retardation, and delusions. Controls had CSF HVA levels intermediate between the two depressed groups. We found no group difference in CSF 5-HIAA and MHPG levels. In individuals with current MDE, those with a history of comorbid alcoholism had lower CSF HVA levels compared with those without a history of alcoholism. Low CSF HVA suggests that impaired dopaminergic activity is associated with a history of alcoholism in persons with current MDE.
In Situ TEM Studies of Nanoparticle Growth in a Fluorozirconate (ZBLAN) Glass Matrix.

ZBLAN (Zirconium, Barium, Lanthanum, Aluminum, and Sodium Fluorides) glass-ceramic materials are being developed as an imaging plate mainly for medical applications [1]. The materials are doped with europium and chlorine and can be heat treated in such a way that they form a novel nanocomposite material containing barium chloride nanocrystals, with the ability to convert ionizing radiation (usually x-rays) into stable electron-hole pairs. The image can be read out afterwards with a scanning laser beam in a so-called “photostimulated luminescence” (PSL) process.
Rho/ROCK and Cdk5 effects on phosphorylation of a β-thymosin repeat protein in Hermissenda

Abstract Rho GTPases acting through effector proteins regulate actin dynamics and cytoskeletal structure. In Hermissenda Csp24 is a cytoskeletal-related protein that contributes to the development of intermediate-term memory, and is homologous to other β-thymosin-like repeat proteins containing multiple actin-binding domains. We have examined the role of Rho GTPase activity and its downstream target ROCK, and cyclin-dependent kinase 5 (Cdk5) on the phosphorylation of Csp24 using 32PO4 labeling of proteins separated with 2-D PAGE. The ROCK inhibitor Y-27632 significantly increased Csp24 phosphorylation, and the Rho activator lysophosphatidic acid (LPA) or the Cdk5 inhibitor butyrolactone significantly decreased Csp24 phosphorylation. Pretreatment with Y-27632 before LPA application significantly reduced the decreased phosphorylation of Csp24 normally detected in nervous systems exposed to LPA. Using a pull-down assay we found that LPA treatments activated Rho and exposure to 5-HT decreased Rho activity. Our results indicate that the Rho/ROCK and Cdk5 signaling pathways contribute to the regulation of Csp24 phosphorylation.
High-resolution anoscopy targeted surgical destruction of anal high-grade squamous intraepithelial lesions: a ten-year experience.

This study was designed to determine whether high-resolution anoscopy and targeted surgical destruction of anal high-grade squamous intraepithelial lesions is effective in controlling high-grade squamous intraepithelial lesions while preserving normal tissues. Retrospective review of 246 patients with high-grade squamous intraepithelial lesions treated with high-resolution anoscopy-targeted surgical destruction from 1996 to 2006, with at least one follow-up at a minimum two months with physical examination, high-resolution anoscopy, cytology, and biopsy when indicated. Lesions were extensive in 197 patients (81 percent); 207 (84 percent) were men, and 194 (79 percent) were immunocompromised (HIV or other). Persistent disease occurred in 46 patients (18.7 percent), requiring planned staged therapy; 10 required surgery. Recurrent high-grade squamous intraepithelial lesions occurred in 114 patients (57 percent) at an average 19 (range, 3–92) months; 26 of these required surgery. All other patients were retreated in-office with high-resolution anoscopy-directed therapies. Complications were seen in nine patients (4 percent). Despite treatment, three patients progressed to invasive cancer (1.2 percent). At their last visit, 192 patients (78 percent) had no evidence of high-grade squamous intraepithelial lesions. High-resolution anoscopy-targeted destruction combined with office-based surveillance and therapy is effective in controlling high-grade squamous intraepithelial lesions and is superior to reports of expectant management or traditional mapping procedures.
Arizonasaurus and its implications for archosaur divergence

The Moenkopi Formation has yielded partial and isolated remains of important archosaurs including rauisuchian skull fragments and isolated poposaur centra and pelvic girdle elements. A recently discovered skeleton referable to Arizonasaurus babbitti shows that most of these archosaurian remains belong to one taxon. Characteristics of the skeleton of Arizonasaurus show that it belongs to a poorly known group of Middle Triassic (240-230 Myr ago) archosaurs called the ctenosauriscids, and that ctenosauriscids are or are closely related to poposaurs. Furthermore, many characteristics of Arizonasaurus provide evidence that poposaurids and ctenosauriscids are derived rauisuchians. The presence of a poposaurid in the early Middle Triassic suggests that the divergence of birds and crocodiles occurred earlier than previously thought. Middle Triassic ctenosauriscids also allow the correlation of Triassic faunas in Europe, Asia, North America and Africa. The Moenkopi Formation fauna represents a transitional fauna between Early and Late Triassic faunas.
Why Oregon patients request assisted death: family members' views.

BACKGROUND Physician assisted death (PAD) was legalized through Oregon’s Death with Dignity Act in 1994 and enacted in 1997.
Evidence of conventional superconductivity in La-Ba-Cu-O compounds.

First-principles methods are applied to investigate the electronic structure and electron-phonon coupling in the end-point members (x=0 and x=1) of the new high-transition-temperature (${T}_{c}$) superconductor ${\mathrm{La}}_{2\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Ba}}_{\mathrm{x}}$${\mathrm{CuO}}_{4}$ and their counterpart cubic perovskites ${\mathrm{La}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Ba}}_{\mathrm{x}}$${\mathrm{CuO}}_{3}$. Alloying with Ba (x=1) induces non-rigid-band changes in the Cu and O density of states, but the Cu charge state changes rather little. The calculated McMillan-Hopfield parameter \ensuremath{\eta} coupled with soft phonon modes provides a strong electron-phonon interaction \ensuremath{\lambda}\ensuremath{\sim}2.5 that can account for the high ${T}_{c}$ of \ensuremath{\sim}30\char21{}40 K in these systems.
The affective impact of field experience education on college students

Field experience education encompasses a wealth of undergraduate curricular opportunities, including cooperative education, internships, adventure learning, and study abroad. Studies of field experiences may be organized according to three stages of the experiential process: selection factors prior to the experience, immediate change due to the experience, and the persistence of change following the experience. Compared to traditional campus activities, field experiences appear to have some significant affective impact on college students. However, a knowledge of experimental design techniques makes obvious the need for a major revision of the manner in which field experiences have been evaluated.
Plant δ15N values along a fog gradient in the Atacama Desert, Chile

The Atacama Desert is characterized by a fog zone occurring between 500 and 800m elevation. We hypothesized that atmospheric deposition from marine sources was the primary source of nitrogen for plants in the fog zone, and so the δ 15 N of plants should differ between those above and below that zone. No significant differences in leaf δ 15 N values were detected among the three locations. The δ 15 N values for non-nitrogen fixing species (6–12‰) were substantially more positive than that of atmospheric deposition (−1‰) suggesting immediate assimilation of nitrogen from fog was not an important source of plant nitrogen.
Estrogen receptor affinity and location of consensus and imperfect estrogen response elements influence transcription activation of simplified promoters.

We have examined the ability of estrogen receptor (ER) to bind and bend DNA fragments containing the Xenopus laevis vitellogenin A2 estrogen response element (ERE), which contains a palindromic, consensus ERE sequence, the X. laevis vitellogenin B1 ERE2, which contains a 1-bp mismatch in the 5'-end of the half-palindrome, and the human pS2 ERE, which contains a 1-bp mismatch in the 3'-end of the half-palindrome. ER binding induced a 65 degrees bend in DNA fragments containing the consensus ERE, the vitellogenin B1 ERE2, or the pS2 ERE. However, ER affinity for the consensus ERE was 2-fold greater than for either the vitellogenin B1 ERE2 or the pS2 ERE. When Chinese hamster ovary (CHO) cells were transfected with reporter plasmids containing either the consensus ERE, the vitellogenin B1 ERE2, or the pS2 ERE separated from the TATA sequence by 26 helical turns, exposure to 10 nm 17 beta-estradiol increased transcription 12.7-, 2.4-, and 3.8-fold, respectively. Increasing the spacing between the ERE and TATA...
California Blueschists and the Tectonostratigraphic Terrane Concept: ABSTRACT

Glaucophane and related schists are present as tectonic fragments in ophiolite-decorated suture zones and as discrete lithotectonic belts along the accreted Mesozoic/Tertiary California margin. Occurrences include parts of the Klamath Mountains, the western Sierran foothills, the Coast Ranges, faulted margins of the Mojave Desert, the Transverse Ranges, and the southern California borderland. Blueschist assemblages formed under high-pressure, low-temperature metamorphic conditions, reflecting the thermal regime of subduction zone environments. Considerable underflow accompanied rifting, drifting, and assembly of far-traveled tectonostratigraphic terranes, as documented by sea-floor magnetic anomaly patterns and age relationships of the oceanic crust-capped lithosphere; th eastern limbs of paleo-Pacific plates (Farallon-Cocos, Kula, etc), have been extensively or completely overridden by the westward encroaching North American plate--7,000 km (4,300 mi) since the Early Cretaceous, and nearly 10,000 km (6,200 mi) since the Jurassic. Thus, although substantial northward drift brought exotic oceanic and continental materials to the growing California crust and caused extensive dislocation in the late Mesozoic and Cenozoic, much plate motion evidently involved a large component of convergence and eastward underflow, as indicated by preserved remnants of high-pressure mineral assemblages scattered throughout California, as well as by the construction of roughly contemporaneous calc-alkaline volcanic-plutonic belts. Subduction appears to have been the dominant rocess attending accretion of the California continental margin. End_of_Article - Last_Page 474------------
Criteria for solid solution formation in nfe alloys

Abstract The first order, nearly free electron theory of metals is applied to homovalent, random, binary alloys. It is found that the volume dependent energy of mixing for such alloys can never be negative, though it can be quite small. The fundamental parameter that determines the volume dependent properties of metals and alloys is an ionic core radius (related to the cut-off radius of the empty core potential) which can be computed from the density of the pure metals. It was found that systems for which the theoretical energy of mixing was less than 10−3 Rydbergs per valence electron form solid solutions, while others do not. This result is easily expressed as a requirement that the ion core radii differ by less than ~ 13% for divalent alloys and ~ 20% for monovalent alloys. Application of these criteria to a large number of alloys shows that they predict whether or not extensive solid solution will take place with reasonable success. The theory also shows that Vegard's law is very nearly valid in NFE random alloys. This is in general agreement with experiment.
Perforin expression by thyroid-infiltrating T cells in autoimmune thyroid disease

Infiltration of the thyroid gland by lymphocytes is a hall-mark of autoimmune thyroid disease; it is particularly evident in Hashimoto's thyroiditis but is also seen in most patients with Graves' disease. Infiltrating cells are comprised primarily of T lymphocytes, of which only a minority appears to be activated. Their precise pathogenic role is largely unknown. Since perforin has been a marker for functionally activated cytotoxic T cells in situ we elected to assess the presence of perforin-containing cells in thyroid-infiltrating lymphocytes and establish their phenotype. Cells were isolated from seven subtotal thyroidectomy specimens, five from patients with Graves' disease and two with Hashimoto's thyroiditis. The novel findings were as follows: CD4+ perforin-containing T cells occurred only in Hashimoto's glands, suggesting a class II-restricted component of cytotoxicity; in Graves' disease, and to a lesser extent in Hashimoto's, perforin-expressing cells were primarily T cell receptor alpha beta- CD4-CD8- (double negative); double negative perforin-containing cells in peripheral blood of normal individuals were largely gamma delta + T cells. In Hashimoto's samples, the predominant population of T cells expressing perforin was CD8+. By comparison, in studies of the synovial fluid of knee joints from patients with rheumatoid arthritis only a minor population of the perforin-containing cells was double-negative. The data suggest significant differences in cytotoxic autoimmune mechanisms between the two autoimmune thyroid diseases. Functional characterization of double-negative T cells is necessary to define their role in autoimmunity.
Does exhaustive search for microcalcifications improve diagnostic yield in stereotactic core needle breast biopsies

Stereotactic core needle biopsy (SCNB) of the breast is a cost-effective alternative to needle localization biopsy for the diagnosis of mammographic calcifications. We questioned whether an exhaustive search for calcium in the small samples obtained in SCNB yields more diagnostic information than that obtained with examination of a standard number of sections. We retrospectively reviewed 168 specimens from 123 patients with mammographic calcifications, including cases in which radiographic suspicion ranged from low to high. Microcalcifications were identified on three initial levels in 112 specimens. Additional sections were examined in 50 specimens. The final diagnosis differed from the diagnosis based on three levels in 11/50 cases (22%). In 6/50 (12%), complete sectioning yielded a specific diagnosis. The increase in technical cost associated with the additional levels was 414% per case. We conclude that exhaustive searching for microcalcifications in SCNB yields a small increase in specific diagnostic information and a high technical cost. In individual cases, the additional information may be critical for appropriate patient management.
Bogoliubov modes of a dipolar condensate in a cylindrical trap

The calculation of properties of Bose-Einstein condensates with dipolar interactions has proven a computationally intensive problem due to the long range nature of the interactions, limiting the scope of applications. In particular, the lowest lying Bogoliubov excitations in three-dimensional harmonic trap with cylindrical symmetry were so far computed in an indirect way, by Fourier analysis of time-dependent perturbations, or by approximate variational methods. We have developed a very fast and accurate numerical algorithm based on the Hankel transform for calculating properties of dipolar Bose-Einstein condensates in cylindrically symmetric traps. As an application, we are able to compute many excitation modes by directly solving the Bogoliubov-De Gennes equations. We explore the behavior of the excited modes in different trap geometries. We use these results to calculate the quantum depletion of the condensate by a combination of a computation of the exact modes and the use of a local density approximation.
Functional interplay between ATM/ATR-mediated DNA damage response and DNA repair pathways in oxidative stress

To maintain genome stability, cells have evolved various DNA repair pathways to deal with oxidative DNA damage. DNA damage response (DDR) pathways, including ATM-Chk2 and ATR-Chk1 checkpoints, are also activated in oxidative stress to coordinate DNA repair, cell cycle progression, transcription, apoptosis, and senescence. Several studies demonstrate that DDR pathways can regulate DNA repair pathways. On the other hand, accumulating evidence suggests that DNA repair pathways may modulate DDR pathway activation as well. In this review, we summarize our current understanding of how various DNA repair and DDR pathways are activated in response to oxidative DNA damage primarily from studies in eukaryotes. In particular, we analyze the functional interplay between DNA repair and DDR pathways in oxidative stress. A better understanding of cellular response to oxidative stress may provide novel avenues of treating human diseases, such as cancer and neurodegenerative disorders.
Interaction process analysis changes accompanying operant conditioning of verbal frequency in small groups.

Summary.-In an experiment with 4-person discussion groups in which the initially most submissive group member was reinforced for speaking and the others punished, an Interaction Process Analysis was made of the operant and con- ditioning discussions. The analysis strongly suggests a differential change in the interaction categories, contingent on the reinforcements and punishments. The experimental situation appeared to produce a tense leader with a quite diffident style. In a recent snidy (Aiken, in press) reward for speaking in small groups sig- nificantly increased verbal output over controls, while punishment produced a non-significant decline. Also, rankings on leadership, participation, quality of ideas, and self-confidence by the punished group members of the rewarded group members showed the latter had improved significantly on all factors, while the rewarded participants' self-judgments were significantly higher on all buc quality of ideas. Using somewhat different procedures, similar changes have been reported by Hastorf ( 1965 ) . Since verbal frequency was being reinforced, the upward shifc in rated leadership and participation were not unanticipated. How- ever, the judged improvernenc in quality of ideas and self-confidence raised a question as to whether systematic verbal content changes might also have taken place during the inceraction. To investigate chis, the Bales Interaction Process Analysis procedures ( 1962 ) were employed."
Fiber Structure Study by Polarized Infrared Attenuated Total Reflection Spectroscopy

Attenuated total reflection (ATR) spectroscopy has been shown to eliminate many of the difficulties encountered in the past with the sample presentation for infrared analysis. Yarn orientation behavior at different draw ratios was studied by analysis of polarized Infrared spectra. The data demonstrate that the α conformation increases with drawing for nylon 6,6 fibers. The chain conformation and crystallite orientation which occur during drawing of nylon 6,6 fibers are also demonstrated. The structural changes observed by the present technique seem to agree well with x-ray diffraction data.
SERRS of azurin adsorbed on a silver surface

Surface-enhanced resonance Raman (SERR) spectra of azurin, a copper-containing protein, were measured on a silver surface with a double grating. Significant differences in intensity and band wavenumber were obtained between SERR and solution resonance Raman spectra in the region 250–300 cm−1 and near 400 cm−1. Preliminary interpretation of these differences suggests a likely orientation of the azurin protein on the silver surface in which the N(His44)N(His115)S(Met119) plane is perpendicular to the metal surface and the imidazole group of His115 is in close proximity to the metal.
Using Percentiles to Communicate Snowfall Uncertainty

AbstractAn objective technique to determine forecast snowfall ranges consistent with the risk tolerance of users is demonstrated. The forecast snowfall ranges are based on percentiles from probability distribution functions that are assumed to be perfectly calibrated. A key feature of the technique is that the snowfall range varies dynamically, with the resultant ranges varying based on the spread of ensemble forecasts at a given forecast projection, for a particular case, for a particular location. Furthermore, this technique allows users to choose their risk tolerance, quantified in terms of the expected false alarm ratio for forecasts of snowfall range. The technique is applied to the 4–7 March 2013 snowstorm at two different locations (Chicago, Illinois, and Washington, D.C.) to illustrate its use in different locations with different forecast uncertainties. The snowfall range derived from the Weather Prediction Center Probabilistic Winter Precipitation Forecast suite is found to be statistically reli...
Research algorithms for emergency medicine

The computer-instigated development of graphic depictions showing rationales and decisions required in the care of patients has allowed clinicians to standardize science in the art of clinical medicine. Such condensation of medical judgment and information into algorithms is particularly important for emergency medicine. This paper describes the background and development of such algorithms in a research setting, and suggests modes for adaptation to clinical settings.
RESTRUCTURING INTERNATIONAL JOINT VENTURES

We present a model of the international joint venture (IJV) restructuring process and discuss, from a single partner firm's perspective, the steps involved in recognizing a need for restructuring and deciding to restructure. In addition, we examine the organizational processes involved in recognizing a need for restructuring and deciding to restructure, and develop propositions about factors that increase the likelihood that a partner firm will decide to restructure its IJV in response to a genuine need for restructuring. We also note the research implications of our work and its contributions to management practice.
THE NEURONAL PROGENITOR CELLS OF THE FOREBRAIN SUBVENTRICULAR ZONE : INTRINSIC PROPERTIES IN VITRO AND FOLLOWING TRANSPLANTATION

Abstract During the development of the central nervous system, progenitor cells, located within distinct germinal zones, produce presumptive neurons that migrate to their destinations and differentiate. Recent studies have demonstrated that a discrete region of the anterior part of the postnatal subventricular zone (SVZa) comprises neuronal progenitor cells whose progeny are fated to become the interneurons of the olfactory bulb. The SVZa is of particular interest because it is one of few germinal zones to persist postnatally and may be the only postnatal germinal zone to give rise exclusively to neurons. To the extent that the SVZa is unique among proliferative zones, the SVZa progeny are unique among neurons. First, unlike most cortical neurons, the SVZa-derived cells do not rely on radial glia-assisted migration when traveling to their target region. Second, the SVZa progeny continue to proliferate as they migrate to their target region. And third, the SVZa progeny express early neuron-specific antigens prior to their final division and, therefore, prior to reaching their destination where they will terminally differentiate. To better understand the capacity of the SVZa progeny to concurrently proliferate, migrate, and differentiate, we studied the cellsin vitroand following transplantation into the neonatal SVZa and adult striatum. In each setting, we found that the SVZa cells continue both to proliferate and to differentiate into neurons. In addition, after homotopic and heterotopic transplantation, we found that the SVZa cells maintain their ability to migrate. These results suggest that the unique features of the SVZa progeny are specified intrinsically rather than by their extrinsic environment.
Pressure-induced degenerate frequency resonance in four-wave light mixing.

Phase-matched four-wave mixing in sodium vapor with a helium buffer gas is carried out in a noncoplanar geometry. The directions of the four light beams remain nondegenerate even if all frequencies are equal. A sharp zero-difference frequency resonance in the intensity of the parametrically generated fourth beam by three incident beams is observed that is proportional to the square of the pressure of the buffer gas. A theoretical interpretation of this effect caused by elimination of destructive interference between two coherent pathways is presented.
Computational modeling of laser-induced self-organization in nanoscopic metal films for predictive nanomanufacturing

Computer models that accurately predict the dynamics of nanoscale self-organization are vital towards knowledge-based nanomanufacturing. Here we present a first principles computational model of laser induced self-organization of thin metallic films (thickness <= 30 nm ) into nanoscale patterns which eventually evolve into ordered nanoparticles. The pattern formation is initiated by a thin film hydrodynamic instability and the ensuing length scales are related to the intrinsic materials properties such as surface tension and van der Waal's dispersion forces. We discuss a fully implicit, finite-difference method with adaptive time step and mesh size control for the solution of the nonlinear, fourth-order PDE governing the thin film dynamics. These simulations capture the changing morphology of the film due to the competition between surface tension and van der Waals forces. Simulation results are used to understand the nonlinear amplifcation of film height perturbations ~(KT/γ) 1/2 , where K, T and γ represent the Boltzmann constant, absolute temperature, and surface tension respectively,leading eventually to film rupture.
Impaired arterial function associated with thinning of cortical bone in rheumatoid arthritis.

Objective To evaluate the association between peripheral arterial function and cortical bone thickness in rheumatoid arthritis (RA). Methods In a cross-sectional study, we measured the combined cortical thickness (CCT) of the second metacarpal bone from hand radiographs, and the ankle-to-arm systolic blood pressure ratio, also known as ankle–brachial index (ABI), in RA patients. We evaluated the association between the 2 using multinomial logistic regression. Results We obtained CCT and ABI measurements in 588 RA patients. The mean ± SD CCT was 3.62 ± 1.16 mm. The proportion of patients with ≥1 ABI value ≤0.9, indicating obstructed lower limb arteries, increased from 18 (9.2%) of 191 patients in the highest CCT tertile to 25 (12.5%) of 200 in the middle CCT tertile to 38 (19.2%) of 198 in the lowest CCT tertile (P for trend 0.005). We noted a similar pattern for ABI values >1.3, indicative of arterial incompressibility (frequencies in high, middle, and low CCT tertiles were 4.7%, 9.5%, and 19.9%, respectively; P for trend ≤0.001). These trends remained significant after multivariable adjustment for potential confounders. After adjustment for the manifestations of RA and cumulative glucocorticoid dose, the association between CCT and arterial obstruction remained significant, but that with arterial incompressibility weakened considerably. Conclusion There is an association between metacarpal cortical bone thinning and obstruction or incompressibility of the peripheral arteries in RA. The association with incompressibility may be mediated by systemic inflammation and/or glucocorticoids, but that with obstruction is independent of a wide array of potential confounders. Clinicians should be alert to the possibility of impaired arterial function RA patients with thinned metacarpal cortical bone.
Dear President Clinton.

YOU are to be congratulated for recognizing the gravity of the crisis in health care. But please do not try to present a detailed plan for health care within 100 days. The problems are too complex and the public's understanding of them is too imperfect. Instead, you should present to the Congress and the public a clear statement of, and rationale for, your goals for health care and your basic approach to achieving these goals. If your goals include covering all Americans for a package of essential services, sharing the costs of this package fairly, and slowing significantly the rate of growth of health expenditures, do not imagine that incremental reform of the present system can do the job. Only comprehensive change in finance and organization has a chance of success. The public, however, is not ready for comprehensive change. Most Americans have health insurance. Most Americans are satisfied with
The “Coffee Doctors”: The Language of Taste and the Rise of Rwanda's Specialty Bean Value

The emergence of Rwanda's specialty coffee sector during the early twenty-first century has brought high-end Rwandan coffee to the shelves of coffee retailers across the United States, Europe, and Japan. While a variety of factors have influenced the rapid development of Rwanda's specialty coffee industry, one of the most significant has been the training of domestic coffee tasters. Known as cuppers, these taste professionals act as a unique link in this global foodway and help enable perception of locally based flavors through marketplace mechanisms. The Rwandan cupper is not simply another middleman in a very long commodity chain. Rather, she or he plays a new role in transforming a generic cash-crop commodity into locality-based luxury item. This new role highlights the language and standards used to differentiate coffees in producing countries for international niche markets.
Low power design under parameter variations

Design considerations for low-power operations and robustness with respect to variations typically impose contradictory design requirements. Low-power design techniques such as voltage scaling, dual-Vth and gate sizing can have large negative impact on parametric yield under process variations . In this tutorial, we focus on circuit/architectural design techniques for low power under parameter variations. We consider both logic and memory design and encompass modeling, analysis as well as design methodology to simultaneously achieve low power and variation tolerance. Design techniques to minimize power under parametric yield constraint as well as major process adaptation techniques using voltage scaling, adaptive body biasing or logic restructuring will be presented. Techniques to deal with within-die parameter variations in logic and memory circuits primarily caused by random dopant fluctuations will be discussed. Finally, we will discuss temperature-aware design, dynamic adaptation to temperature and on-going research activities on low-power and variation tolerant multi-core processor design.
Q 4:24 revisited

Q 4:24 has presented a challenge to classical exegetes and modern scholars alike. Examining Quranic evidence and the exegetical tradition, this article offers a textual analysis of this verse and suggests a new reading. I argue that the first part of Q 4:24 is an independent sentence; that an erroneous reading of it as a continuation of the previous verse led to the replacement of the original meaning of muhsināt ( chaste women ) with married women ; and that there is a strong case for understanding the second part of the verse as addressing mut'a .