cssi/SciSciGPT-SciSciNet huggingface dataset:
Straightforward clustering of single-cell RNA-Seq data with t-SNE and DBSCAN

Abstract Clustering of cells by cell type is arguably the most common and repetitive task encountered during the analysis of single-cell RNA-Seq data. However, as popular clustering methods operate largely independently of visualization techniques, the fine-tuning of clustering parameters can be unintuitive and time-consuming. Here, I propose Galapagos, a simple and effective clustering workflow based on t-SNE and DBSCAN that does not require a gene selection step. In practice, Galapagos only involves the fine-tuning of two parameters, which is straightforward, as clustering is performed directly on the t-SNE visualization results. Using peripheral blood mononuclear cells as a model tissue, I validate the effectiveness of Galapagos in different ways. First, I show that Galapagos generates clusters corresponding to all main cell types present. Then, I demonstrate that the t-SNE results are robust to parameter choices and initialization points. Next, I employ a simulation approach to show that clustering with Galapagos is accurate and robust to the high levels of technical noise present. Finally, to demonstrate Galapagos’ accuracy on real data, I compare clustering results to true cell type identities established using CITE-Seq data. In this context, I also provide an example of the primary limitation of Galapagos, namely the difficulty to resolve related cell types in cases where t-SNE fails to clearly separate the cells. Galapagos helps to make clustering scRNA-Seq data more intuitive and reproducible, and can be implemented in most programming languages with only a few lines of code.
Nutrition in Adolescence

Adolescence features a dramatic set of physical, cognitive, and social changes that alters and intensifies the need for good nutrition while concurrently allowing the individual to make more autonomous decisions about eating behaviors. Studies suggest that healthy diet patterns can deteriorate across adolescence, and recent historical shifts in many nations further complicate efforts to maintain good eating habits. Researchers are beginning to demonstrate how these historical and maturational trends can be reversed to help adolescents maintain nutritional patterns that will foster healthy development through adolescence.
An electro-swing approach

Carbon capture typically relies on pressure or temperature swings for uptake and release of CO2. Researchers now present a device exploiting electrochemistry to drive these processes in an electro-swing approach that grants flexibility for coupling to intermittent energy resources and may have broad applications for carbon capture.
Determination of Objective Analysis of Juiciness among Multiple Beef Muscles and Quality Grades

ObjectivesThe purpose of this study was to use a developed objective juiciness analyses including corresponding tenderness measurements to determine the juiciness among multiple beef muscles of various quality grades.Materials and MethodsTreatments were obtained from 5 different beef sub-primals: Strip loins (IMPS #180), inside rounds (IMPS #169), bottom rounds (IMPS #171B), shoulder clods (IMPS #114), and chuck rolls (IMPS #116). Sub-primals were also represented by 3 different USDA quality grades: Prime, Low Choice and Select; (n = 10/quality grade). All sub-primals were vacuum packaged, aged for 21dthen fabricated into 2.5 cm thick steaks from respective cuts: Adductor (AD), Biceps femoris (BF), Chuck Eye (CE), Infraspinatus (IF), Semimembranosus (SM), Serratus ventralis (SV), Longissimus lumborum (LD), and Triceps brachii (TB). The steaks were frozen (–20°C) until subsequent analyses. Several objective measures of juiciness and tenderness were evaluated on raw and cooked samples. Analysis techniques measured on raw samples included: pH and percentage fat, moisture, protein and collagen. Cooked techniques evaluated included: Warner-Bratzler shear force (WBSF), slice shear force (SSF), cook loss, and pressed juice percentage (PJP). For cooked analysis, each steak was cooked on a clam-shell grill to a medium degree of doneness (71°C), and the fiber orientation (45 or 90°) was determined before sampling. Analysis of PJP was evaluated using a compression-based juiciness method. Following SSF, a 1cm thick PJP slice was removed parallel with predetermined muscle fiber orientation (45 or 90°) and compressed on filter paper at 8 g for 30s. Data were analyzed using the GLIMMIX procedure of SAS (SAS Inst. Inc., Cary, NC; ɑ = 0.05). Subprimal was experimental unit, and muscle, quality grade, muscle × quality grade were used as fixed effects. Carcass was used as a random effect.ResultsA muscle × quality grade interaction (P 0.05) to IF in the Select grade. Within Prime and Low Choice, moisture was greatest (P 0.05) to AD. The pH was lowest (P 0.05) to Choice TB, LD and Select TB. A muscle × grade interaction (P < 0.05) was found for SSF. The BF across all quality grades was the toughest (P < 0.05). The SV was the most tender (P < 0.05) in Prime, however few differences were found in all other quality grades between muscles of AD, IF, LD, and SV. Quality grade and muscle affected (P < 0.05) WBSF and PJP. As quality grade increased, WBSF values decreased (P < 0.05). The SV and CE were more tender (P < 0.05) than AD, TB, and IF. The PJP was less (P < 0.05) for Prime and Choice than Select, while TB and SM were greater (P < 0.05) than IF and AD for the same trait.ConclusionObjective juiciness and tenderness measures among different beef cuts and quality grades cooked to the same degree of doneness indicated that there is a difference in the amount of juice that is released from various beef muscles.
Do-it-Yourself Activities and Subjective Well-Being

We examined predictors of subjective well-being (SWB) associated with do-it-yourself (DIY) activities in a sample of 525 self-identified DIYers through Amazon’s Mechanical Turk. We hypothesized that positive mood, feeling energized or aroused, and experiencing flow during DIY activities, would each contribute to subjective well-being (SWB), and, that negative self-focus would not. We also controlled for individual differences that could affect the experience of negative self-focus and flow: quiet ego and depression/anxiety. Overall, participants identified most with DIY activities that involved aesthetics, repair, upkeep and maintenance, and landscape or gardening, and construction; they reported these activities were challenging and utilized their skills. Using structural equation modeling, we examined our hypothesized model and two alternate models. Our amended hypothesized model accounted for 61% of the variance in SWB. Positive mood/arousal was positively associated with SWB. Quiet ego facilitated SWB, both directly and indirectly through the positive mood/high arousal pathway. Depressed and anxious mood was negatively associated with flow during DIY activities and SWB; it was also positively correlated with excessive self-focus during DIY activities. Our results lend credence to the idea that DIY activities that induce positive mood and high arousal may benefit SWB. Having a strong quiet ego identity may enhance the benefits associated with DIY activities. Our study contributes to the literature by describing the mechanisms responsible for how DIY activities promote SWB, as well as by explaining the factors that optimize the impact of these experiences.
Learning Individualized Treatment Rules for Multiple-Domain Latent Outcomes

For many mental disorders, latent mental status from multiple-domain psychological or clinical symptoms may perform as a better characterization of the underlying disorder status than a simple summ...
Derivation of Airway Basal Stem Cells from Human Pluripotent Stem Cells

Summary The derivation of tissue-specific stem cells from human induced pluripotent stem cells (iPSCs) would have broad reaching implications for regenerative medicine. Here, we report the directed differentiation of human iPSCs into airway basal cells ("iBCs"), a population resembling the stem cell of the airway epithelium. Using a dual fluorescent reporter system (NKX2-1GFP;TP63tdTomato), we track and purify these cells as they first emerge as developmentally immature NKX2-1GFP+ lung progenitors and subsequently augment a TP63 program during proximal airway epithelial patterning. In response to primary basal cell medium, NKX2-1GFP+/TP63tdTomato+ cells display the molecular and functional phenotype of airway basal cells, including the capacity to self-renew or undergo multi-lineage differentiation in vitro and in tracheal xenografts in vivo. iBCs and their differentiated progeny model perturbations that characterize acquired and genetic airway diseases, including the mucus metaplasia of asthma, chloride channel dysfunction of cystic fibrosis, and ciliary defects of primary ciliary dyskinesia.
Chemical stability and reaction kinetics of thiamine mononitrate in the aqueous phase of bread dough.

Abstract Thiamine is a water-soluble essential micronutrient, and grains are the main source of thiamine in the human diet. Refining processes reduce thiamine content; therefore, many flours are enriched with thiamine. Further processes, such as heating (baking), destabilize thiamine. In doughs, thiamine partitions into the aqueous phase (dough liquor). The objective of this study was to document temperature effects on thiamine degradation reaction kinetics in dough liquor. Two concentrations of thiamine mononitrate (1 and 20 mg/mL) were added to dough liquor (the supernatant of centrifuged bread dough) and control solutions (water and pH 6-adjusted water). Samples were stored at controlled temperatures (25, 40, 60, 70, and 80 °C) for up to 6 months, and thiamine degradation was quantified over time using high-performance liquid chromatography. Thiamine degradation kinetics, including the observed reaction rate constant (kobs) and activation energy (Ea) of degradation, were calculated. Dough liquor ingredients stabilized thiamine in most cases when compared to the pH 6 control solutions, especially in the samples containing more thiamine. Thiamine degradation in dough liquor generally followed similar trends to those in the controls: thiamine degraded more quickly in the 20 mg/mL solutions than in 1 mg/mL solutions (with one exception), and increasing temperature led to increased thiamine degradation. However, kobs ranged from 0.0019–0.22 days−1 in dough liquor and 0.0003–0.46 in control solutions, with differences attributed to interactions with components in the dough liquor. The Ea of thiamine degradation was ~90 kJ/mol in the control samples regardless of vitamin concentration but differed between vitamin concentrations in the dough liquor (95 and 60 kJ/mol in 1 and 20 mg/mL solutions, respectively), indicating that a different degradation pathway may have occurred in dough liquor. The different thiamine stability trends in dough liquor compared to control solutions indicate that food formulation has a substantial impact on the chemical behaviors of thiamine.
A modified Papanicolaou Society of Cytopathology system for reporting respiratory cytology specimens: Implications for estimates of malignancy risk and diagnostic accuracy.

Background In 2016, the Papanicolaou Society of Cytopathology (PSC) proposed a classification scheme for reporting cytologic specimens obtained from the respiratory system. Diagnostic sensitivity, specificity, and risk of malignancy were reported for endobronchial ultrasound guided fine needle aspiration but data for other sampling techniques has been poorly documented. Methods In 2016, a modified version of the PSC guidelines was adopted at the University of Missouri for classification of sputum, bronchial washing, bronchial brushing, and fine-needle aspiration specimens. Specimens assigned to the negative category included all specimens containing evaluatable inflammatory or epithelial cells including benign appearing respiratory epithelium. Only specimens with marked artifactual distortion or obscuring blood or mucus were placed in the non-diagnostic category. Results 672 bronchial washing specimens (479 with histology) and 511 bronchial brushings specimens (324 with histology) were reviewed. Washing specimens were classified as non-diagnostic (3%), benign (73%), atypical (10%), suspicious (4%), and malignant (10%). Bronchial brushing specimens were classified non-diagnostic (0.4%) benign (73%), atypical (6%), suspicious (3%), and malignant (17%). Malignancy risks for bronchial washings were insufficient (50%), benign (38%), atypical (62%), suspicious (83%), and malignant (98%). Risks of malignancy for bronchial brushings were insufficient (0%), benign (32%), atypical (79%), suspicious (75%), and malignant (94%). Conclusion Malignancy risks associated with bronchial washings and bronchial brushings are different than those reported for EBUS FNA. When the benign category includes specimens with "normal" appearing cellular elements, the risk of malignancy is substantial (between 32% and 38%).
Are Spicules Related to Coronal Heating

We suggest that the waxing and waning of chromospheric and coronal heating leads to a dynamic solar atmosphere which, under the right circumstances, may produce spicules. Little is known about the heating process. However, Anderson and Athay (1989a) concluded from their study of chromospheric heating that the heating rate per gram of chromospheric matter is only a small fraction of the heating rate per gram of coronal matter. We postulate that the increased heating rate in the corona is a consequence of heating charged particles as opposed to heating neutral atoms. This leads to a specific degree of hydrogen ionization at which coronal heating begins to predominate over chromospheric heating. It also introduces the likelihood that the waxing and waning of the heating rates will have relatively large consequences in the levels where hydrogen ionization is becoming significant. It is demonstrated that changes in the heating rates are capable of inducing increases and decreases in coronal mass comparable to the mass contained in a typical spicule.
Diurnal co‐occurrence of African elephants and other mammals at a Tanzanian waterhole

In the African savannah, as the dry season progresses andwater sources become limited, mammals go from beingwidely distributed to remaining within close proximity of awater source (Western, 1975; Bailey et al., 1996; Redfernet al., 2003). This may lead to higher levels of inter- andintraspeciﬁc resource aggregation (Thrash, Theron B e.g., elephants: Chamaille´-Jammes et al.,2008).At a water resource, African elephants (Loxodonta afri-cana) may prevent other mammals from accessing watervia interference interactions (Valeix, Chamaille´-Jammes F Valeix et al., 2008b). The effects of apparentresource competition can be minimized by reducing tem-poral or spatial overlap with the more competitive species(Ziv et al., 1993; Tokeshi, 1999). Recently, Valeix et al.(2009) showed that mammalian herbivores spent morepotential drinking time at a waterhole with elephantspresent than absent. Because this increase in time wasrelatively small, they suggest it would not inﬂuence thepopulation dynamics of these mammals. However, thesemammals may arrive at a waterhole and be unwilling orunable to access the water because of elephants.We focused on events where mammals co-occur at awaterhole area with elephants but may not move to thewater to drink with elephant present. We examined thespatial proximity to water during single species andco-occurrence events to determine if restrictions of accessto water by the presence of elephants were stronger in thedry season.
Interplay of T-cell receptor and interleukin-2 signalling in Vγ2Vδ2 T-cell cytotoxicity

Human peripheral blood Vγ2Vδ2 T cells are important for host defence and tumour immunity. Their unusual T-cell receptor (TCR) recognizes small molecule phosphoantigens; stimulated cells produce inflammatory cytokines and are potently cytotoxic for a variety of tumours. However, molecular mechanisms linking phosphoantigen stimulation and cytotoxicity are incompletely understood. We know that isopentenyl pyrophosphate (IPP) activates mitogen-activated protein kinase kinase/extracellular signal-regulated kinase (MEK/Erk) and phosphoinositide 3-kinase (PI-3K)/Akt pathways; specific inhibition of Erk or Akt significantly impairs the functional response to IPP. We now show that interleukin-2 also activates MEK/Erk and PI-3K/Akt pathways but on its own, fails to induce cytokine expression or cytotoxicity. Hence, MEK/Erk and PI-3K/Akt activation are necessary but not sufficient to induce effector responses in Vγ2Vδ2 T cells and a TCR-dependent signal is still required for tumour cell killing. Cyclosporin A, an inhibitor of calcineurin, blocked calcium-dependent nuclear translocation of nuclear factor of activated T cell (NFAT) and significantly reduced IPP-induced cytokine production, degranulation and cytotoxicity. The IPP-induced calcium mobilization and NFAT translocation were necessary to activate Vγ2Vδ2 effector functions; interleukin-2, acting on the MEK/Erk pathway, regulated the strength of these responses. The TCR has a specific role in Vγ2Vδ2 T-cell killing of tumour cells, which is distinct from its role in triggering cellular proliferation in response to phosphoantigens.
A CONSTANS Experience Brought to Light

Many plants bloom in the Spring in response to seasonal changes of day length, a phenomenon called photoperiodism. In their Perspective, [Klejnot and Lin][1] discuss new work that sheds light on photoperiodic flowering ([ Valverde et al .][2]). They explain that light photoreceptors modulate production of the CONSTANS transcription factor such that CONSTANS levels drop during the night due to proteolysis and increase during the day due to stabilization of this transcription factor. [1]: http://www.sciencemag.org/cgi/content/full/303/5660/965 [2]: http://www.sciencemag.org/cgi/content/short/303/5660/1003
Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens

Facultative pathogens have extremely dynamic pan-genomes, to a large extent derived from bacteriophages and other mobile elements. We developed a simple approach to identify phage-derived genomic islands and apply it to show that pathogens from diverse bacterial genera are significantly enriched in clustered phage-derived genes compared with related benign strains. These findings show that genome expansion by integration of prophages containing virulence factors is a major route of evolution of facultative bacterial pathogens.
IL-6 Signaling during Cancer Cachexia Progression: The Female Response

Cachexia arises secondary to many chronic diseases and accounts for about 30% of cancer-related deaths. Cachexia occurs in both sexes, but its etiology and progression have been almost exclusively ...
Smoothed aggregation spectral element agglomeration AMG: SA- ρ AMGe

A two---level smoothed aggregation (or SA) scheme with tentative coarse space constructed by spectral element agglomeration method is shown to provide weak---approximation property in a weighted L2 ---norm. The resulting method utilizing efficient (e.g., polynomial) smoothers is shown to have convergence factor independent of both the coarse and fine---grid mesh---sizes, as well as, to be independent of the contrast (i.e., possible large jumps in the PDE coefficient) for second order elliptic problems discretized on general unstructured meshes. The method allows for multilevel extensions. Presented numerical experiments exhibit behavior in agreement with the developed theory.
Bioarchaeological contributions to the study of violence

The bioarchaeological record has an abundance of scientific evidence based on skeletal indicators of trauma to argue for a long history of internal and external group conflict. However, the findings also suggest variability, nuance, and unevenness in the type, use, and meaning of violence across time and space and therefore defy generalizations or easy quantification. Documenting violence-related behaviors provides an overview of the often unique and sometimes patterned cultural use of violence. Violence (lethal and nonlethal) is often associated with social spheres of influence and power connected to daily life such as subsistence intensification, specialization, competition for scarce resources, climate, population density, territorial protection and presence of immigrants, to name just a few. By using fine-grained biocultural analyses that interrogate trauma data in particular places at particular times in reconstructed archaeological contexts, a more comprehensive view into the histories and experiences of violence emerges. Moreover, identifying culturally specific patterns related to age, sex, and social status provide an increasingly complex picture of early small-scale groups. Some forms of ritual violence also have restorative and regenerative aspects that strengthen community identity. Bioarchaeological data can shed light on the ways that violence becomes part of a given cultural landscape. Viewed in a biocultural context, evidence of osteological trauma provides rich insights into social relationships and the many ways that violence is embedded within those relationships.
Pricing IMF liquidity provision: The value of the IMF liquidity commitment☆

Abstract This paper presents a market-based framework for pricing the International Monetary Fund's commitment to provide liquidity assistance, accounting for the credit risk and the insurance benefit involved in such operations. It is based on the isomorphic correspondence between Fund liquidity and common stock put options. The illustrative numerical examples show that the value of this liquidity guarantee could range between several and three hundreds basis points depending on the borrower's creditworthiness, the volatility of capital flows to the borrowing country, and the amount of funds potentially needed to meet the borrower's external obligations.
A real-time qPCR assay for the detection of the nifH gene of Methanobrevibacter smithii, a potential indicator of sewage pollution.

Aims: To develop a quantitative, real-time PCR assay to detect the nifH gene of Methanobrevibacter smithii. Methanobrevibacter smithii is a methanogenic archaea found in the intestinal tract of humans that may be a useful indicator of sewage pollution in water. Methods and Results: Quantification standards were prepared from Meth. smithii genomic DNA dilutions, and a standard curve was used to quantify the target gene and calculate estimated genome equivalency units. A competitive internal positive control was designed and incorporated into the assay to assess inhibition in environmental extracts. Testing the assay against a panel of 23 closely related methanogen species demonstrated specificity of the assay for Meth. smithii. A set of 36 blind water samples was then used as a field test of the assay. The internal control identified varying levels of inhibition in 29 of 36 (81%) samples, and the Meth. smithii target was detected in all water samples with known sewage input. Conclusions: The quantitative PCR assay developed in this study is a sensitive and rapid method for the detection of the Meth. smithii nifH gene that includes an internal control to assess inhibition. Further research is required both to better evaluate host specificity of this assay and the correlation with human health risks. Significance and Impact of the Study: This research is the first description of the development of a rapid and sensitive quantitative assay for a methanogenic archaeal indicator of sewage pollution.
Two Studies of Spirit Possession in Niger

Spirit Possession and Personhood among the Kel Ewey Tuareg. Susan J. Rasmussen. Cambridge: Cambridge University Press, 1995. 178 pp. Embodying Colonial Memories: Spirit Possession, Power, and the Hauka in West Africa. Paul StoIIer. New York: Routledge, 1995. 226 pp.
The repeating microlensing event OGLE-2003-BLG-095: A plausible case for microlensing of a binary source

The apparently repeating microlensing event OGLE-2003-BLG-095 is analyzed. Data were obtained from the OGLE Internet archive and exist in the public domain. The source is relatively bright, with an unmagnified (but possibly blended) $I$-band magnitude of 15.58, and the signal-to-noise ratio of the data is excellent. The light curve shows two distinct, smooth peaks characteristic of a double microlensing event. It can be modeled as either (1) microlensing by a binary lens or (2) microlensing of a binary source, with the latter model providing a statistically superior fit. However due to apparent low-amplitude variability of the source, the interpretation is somewhat ambiguous. OGLE-2003-BLG-095 is only the second possible case in the literature for microlensing of a well-resolved binary source.
Teacher Interactions in Mainstream Social Studies and Science Classes

This investigation was designed to change teacher-student interactions in middle school social studies and science classes. Eighteen of 35 teacher volunteers received a six-session inservice emphasizing teacher effectiveness variables. Results indicated significant differences between experimental and control teachers on a pre-post contrast, as well as on a follow-up (maintenance) contrast. Differential effects on the science and social studies teachers were seen. Similarities and differences related to student type, independent of the intervention, were obtained.
Error Costs & IP Law

A court in doubt about an ip statute’s scope can err in two ways. It can wrongly narrow the ip right’s reach, or wrongly broaden it. The latter error, however, is worse: A wrongly broadened ip statute effectively creates new property. To correct erroneous broadening, unlike erroneous narrowing, the legislature must thus eliminate a now-established property right. And that is very hard to do. Courts cannot, of course, avoid making at least some mistakes. Courts can, however, prefer the mistakes that are easier, not harder, for the legislature to correct. This essay explores this error-cost-based approach to ip statutes, as well as the more productive judicial-legislative dialogue that the approach promotes. The time is ripe for more effective interbranch dialogue on ip law, for the America Invents Act of 2011 — comprising some of the most significant changes to patent law since the 1952 Patent Act — comes fully into force in March 2013.
Active avoidance learning during bilateral spreading depression

Abstract Rats were surgically prepared with chronic cannula inserts to study the effects of potassium chloride (KCL) induced bilateral spreading depression (BSD) and differing shock intensities on acquisition of an active avoidance response (AAR). A two-way shuttle box was utilized with either a visual or auditory conditioned stimulus (CS). Control animals in both CS conditions acquired the AAR whereas the BSD animals experiencing constant shock in both CS conditions failed. The BSD animals characteristically failed to escape the shock. Increasing the shock intensity induced escape learning and led to acquisition of the AAR. The sound CS was found to be more effective in AAR acquisition for both control animals and BSD animals experiencing increased shock intensities.
Imaging techniques for diagnosis of serious intraabdominal and pelvic infections

Abstract Intraabdominal and pelvic infections can be evaluated by various imaging modalities to assist in proper diagnosis and appropriate therapy. The more commonly employed radiographic modalities used in the evaluation of diverticulitis, appendicitis, pelvic inflammatory disease, and post operative infections are sonography (US) and computed tomography (CT). In diverticulitis, appendicitis, and post operative infections, CT is chosen more frequently than US. This choice is dependent on issues such as patient population and skill of the radiologist. Trans-abdominal and trans-vaginal sonography are the diagnostic modalities of choice in pelvic inflammatory disease and tuboovarian abscess. Both imaging modalities provide guidance for percutaneous drainage, which often results in dramatic clinical improvement.
A COMPARISON OF FREE CHOICE PROFILING AND MULTIDIMENSIONAL SCALING OF VANILLA SAMPLES

In Free Choice Profiling (FCP) each individual panelist creates his own series of descriptors to describe the differences among a set of samples. This is in contrast to multidimensional scaling (MDS) where the panelists assess the similarities among the samples. The objective of this study was to compare the results obtained from two FCP panels (one composed of “sensory-savvy” persons and the other of “sensory-naive” individuals) with MDS results. Vanillin and four vanilla samples each originally at 3-fold, 10-fold and 20-fold concentration were evaluated. On average the sensory-savvy (SS) panelists did not use significantly more descriptors than the sensory-naive (SN) group. However, the terms used by the SS group were more likely to discriminate among the samples than the SN terms. Procrustes analysis indicated that the SN data did not have a true consensus space while the SS data did. The MDS data space was visually similar to the FCP space.
Temperament, social competence, and adrenocortical activity in preschoolers

The relations among temperament, social competence, and levels of a stress-sensitive hormone (salivary cortisol) were examined in two studies of preschoolers children (Study 1, N = 29; Study 2, N = 46). In both studies, we sampled cortisol daily for the initial weeks of school year (Group Formation period) and for several weeks later in the year (Familiar Group period). For each child, we examined two measures of cortisol activity (separately for each period) based on the distribution of cortisol levels across days: (a) median cortisol (50th percentile) and (b) cortisol reactivity (the difference between the 75th and 50th percentile). Median cortisol was modestly stable across periods, but cortisol reactivity was not. Children who showed high cortisol reactivity (75th minus 50th percentile > or = 0.10 micrograms/dl) during the Group Formation period but low-to-normal cortisol reactivity during the Familiar Group period were outgoing, competent, and well liked by their peers. In contrast, children who changed from low/normal to high cortisol reactivity and those who maintained high cortisol reactivity from the Group Formation to Familiar Group period were affectively negative and solitary. Children who showed high median cortisol during the Familiar Group period or over both periods scored lower on a measure of attentional and inhibitory control. Together, these results suggest that relations among temperament, social competence, and neuroendocrine reactivity reflect both individual and contextual differences.
On Atomistic-to-Continuum Coupling by Blending

A mathematical framework for the coupling of atomistic and continuum models by blending them over a subdomain subject to a constraint is developed. Using the framework, four classes of atomistic-to...
Na(+)/H(+) exchanger NHE1 as plasma membrane scaffold in the assembly of signaling complexes.

The plasma membrane Na+/H+ exchanger NHE1 has an established function in intracellular pH and cell volume homeostasis by catalyzing electroneutral influx of extracellular Na+ and efflux of intracel...
Nicotine Exposure Does not Alter Plasma to Brain Choline Transfer

Acute and chronic nicotine exposure in rats is associated with an increase in brain acetylcholine (ACh) transmission. The acquisition of choline for neuronal ACh synthesis occurs primarily via two pathways; first, free choline is transported from the blood across the blood-brain barrier (BBB) and/or second, from synaptic choline generated by either hydrolysis of non-bound ACh or membrane phosphatidylcholine catabolism. To determine if nicotine-induced cholinergic demand is associated with increased choline transport rates into brain, we measured BBB choline transport in naive and S-(-) nicotine exposed rats (acute and chronic, 4.5 mg/kg/d for 1, 14, 21 and 28 d; osmotic minipumps) using the in situ rat brain perfusion technique. No significant changes in choline uptake after acute or chronic nicotine exposure were observed in whole brain or cortex. Of considerable interest was a significant decrease in regional brain choline uptake measured in the hippocampus after chronic nicotine exposure (28 d). Our data suggest that the increased ACh transmission observed after nicotine exposure does not correlate with increased blood-to-brain transfer of choline. Considering these data and previous literature reports, we propose that the additional free choline required under conditions of nicotine exposure (for ACh synthesis) is primarily recruited from membrane phospholipid metabolism.
Differential blood and mucosal immune responses against an HIV-1 vaccine administered via inguinal or deltoid injection

Mucosal immunity is central to sexual transmission and overall pathogenesis of HIV-1 infection, but the ability of vaccines to induce immune responses in mucosal tissue compartments is poorly defined. Because macaque vaccine studies suggest that inguinal (versus limb) vaccination may better target sexually-exposed mucosa, we performed a randomized, double-blinded, placebo-controlled Phase I trial in HIV-1-uninfected volunteers, using the recombinant Canarypox (CP) vaccine vCP205 delivered by different routes. 12 persons received vaccine and 6 received placebo, divided evenly between deltoid-intramuscular (deltoid-IM) or inguinal-subcutaneous (inguinal-SC) injection routes. The most significant safety events were injection site reactions (Grade 3) in one inguinal vaccinee. CP-specific antibodies were detected in the blood of all 12 vaccinees by Day 24, while HIV-1-specific antibodies were observed in the blood and gut mucosa of 1/9 and 4/9 evaluated vaccinees respectively, with gut antibodies appearing earlier in inguinal vaccinees (24–180 versus 180–365 days). HIV-1-specific CD8+ T lymphocytes (CTLs) were observed in 7/12 vaccinees, and blood and gut targeting were distinct. Within blood, both deltoid and inguinal responders had detectable CTL responses by 17–24 days; inguinal responders had early responses (within 10 days) while deltoid responders had later responses (24–180 days) in gut mucosa. Our results demonstrate relative safety of inguinal vaccination and qualitative or quantitative compartmentalization of immune responses between blood and gut mucosa, and highlight the importance of not only evaluating early blood responses to HIV-1 vaccines but also mucosal responses over time.
Phase Equilibria in the System Tl-Ca-Ba-Cu-O. I. Stability of the 2122 Phase Under Conditions of Oxygen Annealing

Results are presented for 850°C oxygen annealing experiments (up to 62 hr) on the 2122 (Tl:Ca:Ba:Cu) oxide phase, with and without intermediate grinding. Samples were characterized by powder X-ray diffraction and a.c. magnetic susceptibility. The 2122 phase appears to be thermodynamically stable in oxygen under conditions of both extensive grinding, and, annealing of long duration. However, onset Tc’s vary from 71 K to 109 K for apparently single-phase 2122 samples with nearly identical X-ray powder patterns, depending upon the heat treatment.
Revisiting Patriarchy: Its Conceptualization and Operationalization in Criminology

In recent decades, patriarchy has increasingly been posited as an explanation for gender differences in crime and victimization. While researchers frequently allude to the “patriarchal structure of society” or to “male domination” when discussing their theoretical perspective or findings, rarely do they articulate their conceptualization of the term. As a result, patriarchy has been used as an explanatory wild card that lacks specificity and is purported to both increase and decrease female crime and delinquency. In this paper we examine the conceptualization of patriarchy in criminological theory and research, discuss why the failure to clearly conceptualize this construct is problematic, and offer potential avenues for operationalizing patriarchy with the goal of facilitating future research on gender differences in crime.
Endometrial hyperplasia and the risk of carcinoma

Recent reports suggest that atypical endometrial hyperplasia diagnosed by biopsy or curettage is accompanied by a higher than expected risk of coexistent invasive cancer. In order to test this hypothesis we reviewed the pathology and clinical history of all patients at our institution who underwent hysterectomy for endometrial hyperplasia with or without cytologic atypia. We found 24 patients of 45 with a preoperative diagnosis of hyperplasia with cytologic atypia, and 21 with simple or complex hyperplasia without atypia. No cancers were found at surgery in the latter group nor were any significant historical differences found between the two groups. Of the patients with atypia, 12/24 (50%) had an endometrial carcinoma and nine patients (37.5%) were stage IB or greater. This is a significantly greater risk than previously reported in the literature. Endometrial hyperplasia with cytologic atypia may carry a higher risk of coexistent invasive endometrial carcinoma than previously believed. Methods to identify those patients at highest risk should be determined.
Defects in Microcontact-Printed and Solution-Grown Self-Assembled Monolayers

The structure of microcontact-printed self-assembled monolayers is significant for a number of technological applications as well as for a fundamental understanding of the self-assembly process. The structural differences between printed and solution-deposited monolayers of alkanethiol on Au(111) have been examined utilizing grazing incidence X-ray diffraction and atomic force microscopy. Although the local structures are found to be similar, the domain structure and therefore macroscopic packing of the molecules are found to vary. Surprisingly, printed decanethiol monolayers appear to be significantly better ordered translationally than those formed by standard solution techniques.
A new approach to the Bipartite Fundamental Bound

We consider a bipartite distance-regular graph ΓΓ with vertex set XX, diameter D≥4D≥4, valency k≥3k≥3, and eigenvalues θ0>θ1>⋯>θDθ0>θ1>⋯>θD. Let CXCX denote the vector space over CC consisting of column vectors with rows indexed by XX and entries in CC. For z∈Xz∈X, let zˆ denote the vector in CXCX with a 1 in the zzth row and 0 in all other rows. Fix x,y∈Xx,y∈X with ∂(x,y)=2∂(x,y)=2, where ∂∂ denotes the path-length distance. For 0≤i,j≤D0≤i,j≤D, we define wij=∑zˆ, where the sum is over all vertices zz such that ∂(x,z)=i∂(x,z)=i and ∂(y,z)=j∂(y,z)=j. Define a parameter ΔΔ in terms of the intersection numbers by Δ=(b1−1)(c3−1)−(c2−1)p222. In [M. MacLean, An inequality involving two eigenvalues of a bipartite distance-regular graph, Discrete Math. 225 (2000) 193–216], we defined what it means for ΓΓ to be taut . We show ΓΓ is taut if and only if Δ≠0Δ≠0 and the vectors Exˆ,Eyˆ,Ew11,Ew22 are linearly dependent for E∈{E1,Ed}E∈{E1,Ed}, where d=⌊D/2⌋d=⌊D/2⌋ and EiEi is the primitive idempotent associated with θiθi.
Die Vorteile des Kontaktlinsentragens für Kinder und Jugendliche

Zweck Kindern werden Kontaktlinsen als Korrekturmoglichkeit von Fehlsichtigkeiten nicht annahernd so haufig angeboten wie Jugendlichen. Dieser Beitrag untersucht die Vorteile des Kontaktlinsentragens fur Kinder und Jugendliche, um festzustellen, ob Kinder davon genauso profitieren wie Jugendliche. Falls ja, sollten Kontaktlinsen Kindern routinemasig als Behandlungsmethode fur Fehlsichtigkeiten angeboten werden.
The genetic and economic impact of the CIMMYT wheat breeding program on local producers in the Yaqui Valley, Sonora Mexico

This article quantifies the productivity gain from CIMMYT-released semidwarf bread wheat (Triticum aestivum) cultivars over time, using test plot data from Mexico's Yaqui Valley. Previous studies have shown a deceleration in irrigated wheat yield growth since the 1980s, which could be due to slowing increase in genetic potential. Our results suggest that CIMMYT cultivars contributed a 0.46% annual increase (about 38 kg/ha annually) to wheat yields in the Yaqui Valley, which raised local wheat producers' revenue by an average of $4 million annually for the period 1990 to 2002, and by approximately $9 million in 2002.
Novel Indices for the Topological Complexity of Molecules

Abstract The development of molecular complexity measures is reviewed. Two novel sets of indices termed topological complexities are introduced proceeding from the idea that topological complexity increases with the overall connectivity of the molecular graph. The latter is assessed as the connectivity of all connected subgraphs in the molecular graph, including the graph itself. First-order, second-order, third-order, etc., topological complexities i TC are defined as the sum of the vertex degrees in the connected subgraphs with one, two, three, etc., edges, respectively. Zero-order complexity is also specified for the simplest subgraphs–the graph vertices. The overall topological complexity TC is then defined as the sum of the complexities of all orders. These new indices mirror the increase in complexity with the increase in the number of atoms and, at a constant number of atoms, with the increase in molecular branching and cyclicity. Topological complexities compare favorably to molecular connectiviti...
Novel self-powered pH indicator using ionic polymeric gel muscles

A novel design for a torsional spring-loaded pH indicator using ionic polymeric gel fibrous muscles is presented. The essential parts of the proposed self-powered pH indicator are a pair of co-axial and concentric cylinders, an assembly of fibrous polyacrylonitrile (PAN) muscles, a torsional spring, and a dial indicator. The two co-axial cylinders are such that the inner cylinder may pivotally rotate about the central rotation axis that is fixed to the inner bottom or side of the outer cylinder. The outer cylinder also serves as a reservoir for any liquid whose pH is to be determined either statically or dynamically. The internal cylindrical drum is further equipped with a dial indicator on one of its outer end caps such that when a pH environment is present the contraction or expansion of the PAN fibers cause the inner drum to rotate and thus give a reading of the dial indicator. The motion of the dial indicator may also be converted to an electrical signal (voltage) for digital electronics display and computer control. A mathematical model is also presented for the dynamic response of the self-powered pH indicator made with contractile PAN fiber bundle assemblies.
A Note on Marginal Linear Regression with Correlated Response Data

Abstract Correlated response data often arise in longitudinal and familial studies. The marginal regression model and its associated generalized estimating equation (GEE) method are becoming more and more popular in handling such data. Pepe and Anderson pointed out that there is an important yet implicit assumption behind the marginal model and GEE. If the assumption is violated and a nondiagonal working correlation matrix is used in GEE, biased estimates of regression coefficients may result. On the other hand, if a diagonal correlation matrix is used, irrespective of whether the assumption is violated, the resulting estimates are (nearly) unbiased. A straightforward interpretation of this phenomenon is lacking, in part due to the unavailability of a closed form for the resulting GEE estimates. In this note, we show how the bias may arise in the context of linear regression, where the GEE estimates of regression coefficients are the ordinary or generalized least squares (LS) estimates. Also we explain wh...
Quelques pas à travers de longues routes sinueuses

Suivons un instant le chemin d’Œdipe dans l’Œdipe-Roi de Sophocle, suivons-le en accompagnateurs contemporains du roi – il faudrait plus exactement l’appeler tyran – et donc en lecteurs historiens et philologues. Puisque trois mille ans environ nous en separent, la reconstruction de ce chemin n’est rendue possible ( ?) que par l’immense reserve d’informations, de textes, de methodes qui s’est accumulee pendant tout ce temps : par une enorme bibliotheque, en somme. Trois mille ans de livres vo...
Comparison of responses to adrenomedullin and adrenomedullin analogs in the mesenteric vascular bed of the cat.

Abstract Responses to adrenomedullin, a newly discovered hypotensive peptide isolated from human pheochromocytoma cells, and the carboxy terminal 15–52 (adrenomedullin-(15–52)) and 22–52 (adrenomedullin-(22–52)) amino acid fragments of adrenomedullin were investigated in the mesenteric vascular bed of the cat. Under constant flow conditions, injections of adrenomedullin, adrenomedullin-(15–52), and calcitonin gene-related peptide (CGRP) in doses of 0.003–1 nmol into the perfused superior mesenteric artery caused significant dose-related decreases in mesenteric arterial perfusion pressure. Mesenteric vasodilator responses to adrenomedullin and adrenomedullin-(15–52) were similar in magnitude and duration, while vasodilator responses to CGRP were greater in magnitude and longer in duration than those produced by adrenomedullin or adrenomedullin-(15–52) when these agents were injected in doses of 0.1–1 nmol. Adrenomedullin-(22–52) caused no significant change in mesenteric arterial perfusion pressure when injected in doses up to 10 nmol. These results suggest that amino acids 15–52 and the six-membered ring structure of adrenomedullin are important for the expression of vasodilator activity in the mesenteric vascular bed of the cat.
Dilatant till facilitates ice-stream flow in northeast Greenland

Abstract We present radio-echo sounding (RES), global positioning system (GPS), and active-source seismic data across the central portion of the Northeast Greenland Ice Stream (NEGIS). NEGIS widens downglacier from a small region of high geothermal flux near the ice divide. Our data reveal high-porosity (40+%) water-saturated till lubricating the ice stream. Ice accelerates and thins as it flows into NEGIS, producing marginal troughs in surface topography. These troughs create steep gradients in the subglacial hydropotential that generate parallel “sticky” and “slippery” bands beneath the shear margins. The low-porosity “sticky” sediment bands limit ice entrainment across the margins and thus restrict further widening, producing the long, narrow, and relatively stable ice stream. However, the observed relations among surface elevation, basal water routing, broad sedimentary drape, and till dilatancy suggest that rapid shifts in ice dynamics are possible, including rapid transmission of ocean forcing inland. The source and routing of the subglacial till are unclear, but our data help constrain hypotheses.
A Tutte Polynomial for Partially Ordered Sets

We investigate the Tutte polynomial of a greedoid associated to a partially ordered set. In this case, we explore the deletion-contraction formula in two ways and develop an antichain expansion for the polynomial. We show that the polynomial can determine the number of orders ideals, order filters and antichains of all sizes of a poset P, but neither the number of chains, multichains, extensions, nor the dimension of P. We show how to compute the polynomial for the direct sum, ordinal sum, and ordinal product of two posets, but show that this cannot be done for a direct product. We also show it is possible to determine ?(P*) from ?(P), where P* is the dual poset of P. We also consider the idea of feasible isomorphism of two greedoids and show that two feasibly isomorphic greedoids have the same polynomial.
Total syntheses of korupensamine C and ancistrobrevine B

Abstract The first total syntheses of korupensamine C ( 3 ) and ancistrobrevine B ( 4 ) have been achieved. Important benzyne chemistry related to the construction of the naphthalene moiety, manipulation of methoxy groups on the tetrahydroisoquinoline unit, and hindered biaryl formation are described.