cssi/SciSciGPT-SciSciNet huggingface dataset:
Continuing the Discussion: A Commentary on “Wilderness Therapy: Ethical Considerations for Mental Health Professionals”

Wilderness therapy programs continue to be a possible treatment modality for at-risk youth who require out-of-home care. Issues associated with wilderness therapy also continue to be a spirited topic with professionals in the field and the general public. This commentary will add additional considerations, and continue the discussion concerning wilderness therapy not addressed in the Becker (Child Youth Care Forum, doi. 10.1007/s10566-009-9085-7, 2010 this issue) article. Issues related to cost, safety of clients, effectiveness of programs and proper training of staff will be discussed. Ethical issues faced by mental health providers working with wilderness therapy programs, as discussed in Becker’s article, will also be reviewed.
Thermodynamic theory of metal-insulator transitions

Abstract A theory of electron correlation effects at nonzero temperatures is discussed which successfully describes the set of metal-insulator transitions of the (V 1− x Cr x ) 2 O 3 alloy system in the paramagnetic state.
The proline rich region of the Tec homology domain of ITK regulates its activity

Inducible T-cell kinase (ITK) is a member of the Tec family of tyrosine kinases that are involved in signals emanating from cytokine receptors, antigen receptors and other lymphoid cell surface receptors. Stimulation of tyrosine phosphorylation and activation of ITK by the T-cell antigen receptor, CD28 and CD2 requires the presence of the Src family kinase Lck in T-cells. We have previously demonstrated that the activation of ITK by Src family kinases uses a phosphatidylinositol 3-kinase pathway, which recruits ITK to the membrane via its pleckstrin homology (PH) domain where it is acted upon by Src. We have further explored the mechanism of this requirement for Src family kinases in the activation of ITK. We found that deletion of the proline rich sequence found in the Tec homology domain of ITK results in reduced basal activity of ITK approximately 50%. These differences in the basal activity of ITK were observed when the PH domain was deleted or when the kinase was membrane targeted. Furthermore, this deletion reduces the ability of the Src family kinase Lck to activate ITK, as well as to induce the ITK mediated tyrosine phosphorylation of its substrate PLCγ1. By contrast, deletion of the SH3 domain of ITK resulted in a two-fold increase in the basal activity of ITK, and allowed this mutant to have an enhanced response to Lck. These results suggest that the proline rich region within the Tec homology domain of ITK regulates its basal activity and its response to Src family kinase signals.
Application of spin-orbit theory to a class of orbit-orbit resonances: The case of Titan-Hyperion

The orbit-orbit interaction of two satellites of greatly unequal mass is studied under the condition that the more massive satellite moves in a circular (unperturbed) orbit that lies entirely inside the orbit of the smaller (perturbed) body. It is shown that this system is equivalent in every respect to a special case ofspin-orbit coupling. On this basis, conditions for resonance are derived, as well as libration periods and bandwidths. Application is made to Saturn's resonant pair of satellites, Titan and Hyperion, which approximate the conditions of this problem. The calculated libration period of 646 days is in reasonably good agreement with the observed 640-day period.
Avoid the Mismatch Between Strategy and Strategic Leaders

The decade of the 1980s was the decade of analysis, portfolio management, and process development. The emphasis was on strategic planning and not on strategic leadership. Little attention appears to have been given to ensuring that the right leaders and the right teams were in place to implement the strategies.
Multiple Perspectives on Elementary Teachers' Science Identities: A case study

This narrative case study examined the relationship between teacher identity and elementary science teaching. Teacher identity was described using a modification of Gee's framework incorporating three perspectives: the teachers’ self-described identity, the researchers’ view of teacher identity, and the students’ views of teacher identity. Over the course of one school year, we studied one class of second-grade students receiving science instruction from three different teachers. We found that each teacher had unique identity characteristics. Further, the three perspectives of teacher identity were sometimes in conflict with one another within individual teachers, emphasizing the importance of incorporating multiple perspectives in order to give a complete description of teacher identity. This study has meaningful implications for understanding the ways in which students’ perspectives can enrich our understanding of teacher identity.
Progressive Increases in Complexity of T-Wave Oscillations Herald Ischemia-Induced Ventricular Fibrillation

T-wave alternans (TWA), an ABAB oscillation, has been postulated as the initial pattern in a stepwise progression to higher-order oscillations, culminating in sudden arrhythmic death. The present study is the first to provide experimental evidence to support this intriguing concept. Epicardial and endocardial ECGs from 12 dogs were monitored during 8-minute left anterior descending coronary artery occlusion with right atrial pacing at 150 bpm. TWA magnitude was measured by modified moving average beat analysis, and the complexity of T-wave oscillations was assessed by complex demodulation. In 6 animals with subsequent ventricular fibrillation (VF), TWA achieved a threshold of 5.00+/-1.30 mV in epicardial ischemic-zone electrograms, which then exhibited a stepwise increase in T-wave oscillation complexity to quadrupling (ABCDABCD, 3 cases) or tripling (ABCABC, 2 cases) and to more complex forms (5 cases) preceding VF (6 cases). In dogs without VF, peak TWA levels did not increase from baseline, measuring a maximum of 0.35+/-0.10 mV (P=NS), or only 7% the value of those with VF, and T-wave multupling was not observed (0 of 6 versus 5 of 6, P<0.005). Discordant TWA episodes, with T waves alternating out of phase, were associated with increased T-wave complexity and fibrillation in 4 of 6 dogs with VF but in none of the 6 dogs without VF (P<0.025). TWA appears to be the first step in an orderly progression of T-wave complexity, episodes of discordant TWA, and VF. This demonstrated increase in T-wave complexity points to a fundamental mechanistic link underlying the ability of TWA to predict lethal arrhythmias.
Photoactive Antimicrobial PVA Hydrogel Prepared by Freeze-Thawing Process for Wound Dressing

A freeze-thawing process was employed to produce both rose bengal (RB)/polyvinyl alcohol (PVA) and benzophenone (BP)/PVA hydrogels, respectively. Results indicated that only RB incorporated PVA (RB/ PVA) could form hydrogel after undergoing three cycles of freeze-thawing process; One of the cycles should be conducted by freezing at � 15 � C 6 3 � C for 18 h followed by thawing at 25 � C for 6 h. The structural features and functional properties of the RB/PVA hydrogel were inves- tigated by FTIR, XRD, SEM evaluations, and photo- induced antimicrobial functions were examined as well. Release of RB from the RB/PVA hydrogel was examined by UV-Vis spectroscopy. The freeze-thawed RB/PVA hydrogel showed antimicrobial abilities against both E. coli and S. aureus under the exposure to fluorescence light as well as UVA (365 nm) light. V C 2010 Wiley Periodicals, Inc. J Appl Polym Sci 116: 2418-2424, 2010
Pigment pattern evolution by differential deployment of neural crest and post-embryonic melanophore lineages in Danio fishes

Latent precursors or stem cells of neural crest origin are present in a variety of post-embryonic tissues. Although these cells are of biomedical interest for roles in human health and disease, their potential evolutionary significance has been underappreciated. As a first step towards elucidating the contributions of such cells to the evolution of vertebrate form, we investigated the relative roles of neural crest cells and post-embryonic latent precursors during the evolutionary diversification of adult pigment patterns in Danio fishes. These pigment patterns result from the numbers and arrangements of embryonic melanophores that are derived from embryonic neural crest cells, as well as from post-embryonic metamorphic melanophores that are derived from latent precursors of presumptive neural crest origin. In the zebrafish D. rerio, a pattern of melanophore stripes arises during the larval-to-adult transformation by the recruitment of metamorphic melanophores from latent precursors. Using a comparative approach in the context of new phylogenetic data, we show that adult pigment patterns in five additional species also arise from metamorphic melanophores, identifying this as an ancestral mode of adult pigment pattern development. By contrast, superficially similar adult stripes of D. nigrofasciatus (a sister species to D. rerio) arise by the reorganization of melanophores that differentiated at embryonic stages, with a diminished contribution from metamorphic melanophores. Genetic mosaic and molecular marker analyses reveal evolutionary changes that are extrinsic to D. nigrofasciatus melanophore lineages, including a dramatic reduction of metamorphic melanophore precursors. Finally, interspecific complementation tests identify a candidate genetic pathway for contributing to the evolutionary reduction in metamorphic melanophores and the increased contribution of early larval melanophores to D. nigrofasciatus adult pigment pattern development. These results demonstrate an important role for latent precursors in the diversification of pigment patterns across danios. More generally, differences in the deployment of post-embryonic neural crest-derived stem cells or their specified progeny may contribute substantially to the evolutionary diversification of adult form in vertebrates, particularly in species that undergo a metamorphosis.
Spinal anesthesia in the treatment of megacolon and obstinate constipation

P RIOR to 1927, the treatment of idiopathic megacoIon was varied and extremeIy unsatisfactory. The conservative treatment consisted of diet, catharsis and repeated enemas. The resuhs were far from encouraging and after a Iong tria1, many of these cases were treated surgicaIIy. The surgica1 treatment was attended with radica1 procedures and high mortaIity. The more radica1 procedures varied from coIostomy, partia1 coIectomy to tota extirpation of the coIon. Even after such formidabIe procedures, the resu1t.s were often poor. Various theories have been advanced as to the cause of idiopathic megacoIon ranging from adhesions on the outside of the bowe1 to vaIve formation within. Briefly, some of these theories wiI1 be mentioned. An abnormaIIy Iong mesentery, chronic coIitis, increased Iength of the coIon, actua1 mechanica obstruction and congenita1 aplasia of the muscuIar tunics, were the outstanding theories unti1 rgoo. At that time Fenwick considered the possibiIity of spasm of the sphincter ani associated with fissures in the ana margin. In rgo7, Bing considered a neuropathic diIatation and hypertrophy of the coIon, probabIy a segmenta defect associated with changes in the sympathetic nerves. The true definition of idiopathic megacoIon infers a diIatation of the bowe1 without any obvious mechanica obstruction inside or outside of the bowe1. If we are to adhere to this definition, many of the theories, by the nature of their expression inferring some mechanica obstruction, cannot be considered in a discussion of idiopathic megacoIon. In 1895, Langley and Anderson showed that stimuIation of the Iumbar sympathetic gangIia caused an inhibition of peristaIsis with diIatation of the coIon and contraction of the interna sphincter of the anus. GaskeII feIt that impuIses inhibitory to the muscuIature of the Iarge bowe1 and motor to the interna sphincter of the anus pass through the Iumbar sympathetics. Learmouth and Markowitz have since substantiated this opinion by pIacing a buIb against the interna sphincter and recording contractions foIIowing stimuIation of the gangIia. In 1924, RoyIe and Hunter removed the Iumbar sympathetics for reIief of spastic paraIysis of the Iower extremities. They noted that one of the benefits of the operation was the striking reIief of the obstinate constipation that had been present in these patients. It was not unti1 1926, however, that a practica1 appIication of these observations was made when Wade and RoyIe performed a Iumbar sympathectomy for Hirschsprung’s disease (idiopathic megacoIon). The child made a fine recovery with exceIIent cIinica1 improvement and reIief of the constipation. In 1928, Judd and Adson reported 2 cases and in 1930, Scott and Morton reported one case. Since then numerous cases have been reported with varying degrees of success. The next step in the treatment of the disease was the introduction of spina anesthesia as a preoperative test to determine whether sympathectomy wouId be of benefit. This test was used prior to sympathectomy in the case reported by Scott and Morton. The resuIts were striking.
The rabbi and the psychiatrist: Effective counseling for youth.

Collaboration between a clergyman and a psychiatrist in the treatment of the emotionally disturbed is rare in the literature and certainly not common in practice. Historically, there have been many ideological conflicts between psychiatrists and those trained as religious leaders. The psychiatrist who is critical of such spiritual values as God and religion often fails to appreciate the emotional support that the clergyman can provide. The psychiatrist who disdains identification with or appreciation of the spiritual elements will, in many cases, be as ineffectual as the clergyman who often fails to recognize his own limitations or is unwilling to understand the appropriate role of the psychiatrist. Just as the role of the psychiatrist has changed during the twentieth century, so has that of the clergyman. He no longer is simply the instrument for inspirational guidance; he is confidant, advisor, counselor to the individuals in his congregation and in the community. He does not limit himself to religious scholarship, but is expected to know more about diverse fields of knowledge and to have a broader range of expertise. As a result, the clergyman often feels harassed and inadequate when called upon to perform a variety of functions within his congregation and among his neighbors. This is especially true in the field of mental health. The clergyman's image as a caring and compassionate individual encourages troubled members to seek his guidance. For many, he represents a religious system that gives reassurance as well as claims authority. Because of his human contacts and his role image, he often is given first consideration as a source of comfort if not therapy by the troubled member of his community. The adolescent or young adult in particular is capable of establishing a trusting relationship with him because previous rapport has been established in casual and informal contacts. And like the family doctor, the pediatrician, or the educator, the clergyman is often the first to detect early crises and emotional problems in the adolescent.
Silicon solar-cell processing for minimizing the influence of impurities and defects

Commercial Si solar cells are fabricated on low-cost wafers that contain high concentrations of impurities and defects. To achieve high device efficiency, cell-fabrication processing must include steps that can remove as-grown impurities and defects as much as possible and passivate the remaining. However, to maintain the cost effectiveness, these processes must be included as a part of a typical cell-fabrication sequence without increasing the number of process steps. This paper discusses various solar-cell processing approaches for minimizing deleterious effects of impurities and defects to yield high efficiency.
Isolation of 3,4′,5-trimethoxy-trans-stilbene, otobaene and hydroxyotobain from Virola cuspidata

Abstract Investigation of the petroleum ether extract of Virola cuspidata (Benth.) Warb. led to the isolation of 3,4′,5-trimethoxy- trans -stilbene and the lignans, otobaene and hydroxyotobain. The structure of 3,4′,5-trimethoxy- trans -stilbene was determined on the basis of its u.v. and NMR spectra. Otobaene and hydroxyotobain were identified by comparison of physical data with literature values.
Corporate commercial paper, note issuance facilities, and shareholder wealth

Abstract In this paper, we hypothesize that the financial market regards the issuance of securities through a note issuance facility or a commercial paper program backed by a standby letter of credit as a favorable signal about the issuing firm. This is due to the certification role played by banks. We demonstrate that announcements of commercial paper programs backed by these formal backstop facilities have a statistically significant positive effect on shareholder wealth. This result is in contrast to issues of other types of securities studied in the literature which have been shown to induce nonpositive effects on shareholder wealth. The initiation of commercial paper programs without this backing has little effect on shareholder wealth. Finally, we demonstrate that the quality of the credit ratings associated with these issues of commercial paper has little effect on abnormal returns. Thus, our results cannot be explained by the pattern of these ratings.
Nitrate Absorption and Acetylene Reduction by Soybeans during Reproductive Development

Nodulated and unnodulated soybeans (Glycine max [L.] Merr.) were grown in N-free or N-containing nutrient solutions, respectively. Starting at the initial flowering stage, and throughout reproductive growth, the NO3- absorption capacity of roots of intact plants from both treatments was determined in short-term uptake experiments. Acetylene reduction activity was determined for nodulated plants. Nitrate absorption rate, expressed on a root dry weight basis, was greatest at early flowering for both nodulated and unnodulated plants. At 33 days after germination, the NO3- absorption rate of unnodulated plants was twice as great as that of nodulated plants. During the remainder of the sampling period, NO3- absorption rates of both nodulated and unnodulated plants decreased progressively and similarly. Maximum nodule specific activity occurred 30 days after germination, or initial flowering. However, maximum total C2H2 reduction activity, oner plant basis, was observed during the early stages of pod-filling. Compared to unnodulated plants dependent on NO3- assimilation, nodulated plants were smaller, had less N in vegetative tissues, and produced less seed per plant. We suggest that the higher NO3- absorption rate of unnodulated soybean roots, particularly during early reproductive growth, may have reflected a more favorable supply of photosynthate translocated to the roots from larger, more vigorous, non-N-stressed shoots.
Chemoenzymic Synthesis of N-(Phosphonomethyl)glycine

Permeabilized, metabolically-inactive transformants of the methylotrophic yeasts Hansenula polymorpha and Pichia pastoris which contain significant quantities of the enzymes spinach glycolate oxidase ((S)-2-hydroxyacid oxidase, EC 1.1.3.15), Saccharomyces cerevisiae catalase T (EC 1.11.1.6), and endogenous catalase have been used as catalysts for the oxidation of glycolic acid by oxygen to produce glyoxylic acid in aqueous mixtures containing (aminomethyl)phosphonic acid. After separation and recovery of the microbial catalyst from the oxidation product mixture for reuse, the resulting solution of glyoxylic acid and (aminomethyl)phosphonic acid was subsequently hydrogenated with a palladium/carbon catalyst to produce N-(phosphonomethyl)glycine (glyphosate), a broad-spectrum, postemergent herbicide. Complete conversion of (aminomethyl)phosphonic acid in the hydrogenation allowed the use of a simple acid precipitation for isolation of the N-(phosphonomethyl)glycine from the hydrogenation product mixture in ...
Hiatal shell concentrations, sequence analysis, and sealevel history of a Pleistocene coastal alluvial fan, Punta Chueca, Sonora

Richly fossiliferous marine sediments exposed along the Sonoran coastline of the Gulf of California near Punta Chueca provide an excellent setting in which to test (a) the strength of the association of skeletal concentrations with sedimentary hiatuses, (b) the utility of taphonomic evidence for reconstructing detailed histories of those non-depositional episodes, and thus (c) the largely unexploited potential of skeletal concentrations in the identification and interpretation of lithologically obscure unconformities and condensed sequences in shallow marine deposits. Sequence analysis based on discontinuity surfaces is possible in the complex, alluvial fan-to-shallow marine transition at Punta Chueca despite rapid facies changes. Progradation of depositional sequences that contain cobbles reworked from older terrace deposits indicates accumulation during a fall in eustatic sea level. The supratidal to subtidal conglomerates and sands contain a variety of predominantly molluscan shell concentrations that, on the basis of postmortem histories of shells, formed during periods of low net sedimentation (i.e. depositional hiatuses); the majority of these shell beds lie along discontinuity surfaces identified by independent physical stratigraphic evidence. Although not all discontinuity surfaces in the terrace are paved by shell material. and not all relative concentrations of shells indicate distinct discontinuities, the strength of the association between skeletal concentrations and stratigraphic hiatuses reveals the high degree of control on fossil occurrence by sedimentation rates, and indicates that skeletal concentrations can provide good clues to stratigraphically significant surfaces. Moreover, the detailed dynamics of non-depositional episodes are reliably revealed by taphonomic analysis of the associated fossil assemblages, improving interpretations of non-depositional episodes in local sedimentary history.
VG-13: A nuclear-track-recording glass detector with uniquely high resolution

Abstract We find that tracks of relativistic heavy nuclei as light as lanthanum (Z = 57) can be revealed in VG-13, a commercially available phosphate glass, by etching it in fluoboric, nitric or hydrofluoric acid. A study of its response to relativistic U, Au and La ions at temperatures from −77°C to +20°C shows that the temperature-dependence of the response is one or two orders of magnitude smaller than for track-recording plastic detectors. Ionic charge states corresponding to fully stripped ions, ions with one electron, and ions with two electrons are resolved with standard deviations ranging from −0.1 to 0.25 charge unit. This charge resolution for heavy nuclei exceeds that of any other detector, making possible searches for fractionally charged heavy nuclei in high-energy nucleus-nucleus collisions. It may also be possible, by range and etch rate measurements, to determine the isotopic abundances of iron and heavier elements in cosmic rays.
Cytosolic and nuclear protein targets of thiol-reactive electrophiles.

Reactive electrophiles formed from toxic drugs and chemicals and by endogenous oxidative stress covalently modify proteins. Although protein covalent binding is thought to initiate a variety of adaptive and toxic responses, the identities of the protein targets are generally unknown, as are protein structural features that confer susceptibility to modification. We have analyzed the protein targets in nuclear and cytoplasmic proteomes from HEK293 cells treated in vitro with two biotin-tagged, thiol-reactive electrophiles, (+)-biotinyl-iodoacetamidyl-3, 6-dioxaoctanediamine (PEO−IAB) and 1-biotinamido-4-(4‘-[maleimidoethylcyclohexane]-carboxamido)butane (BMCC). Biotinylated peptides were captured by affinity enrichment using neutravidin beads, and the adducted peptides were then analyzed by multidimensional liquid chromatography−tandem mass spectrometry. A total of 897 adducts were mapped to different cysteine residues in 539 proteins. Adduction was selective and reproducible, and >90% of all adducted prote...
The regulation of cholecystokinin release from rat caudatoputamen in vitro.

Abstract Cholecystokinin (CCK) is one of the most abundant neuropeptides in the rat caudatoputamen (cp). CCK perikarya innervating the cp are thought to originate in neurons in the claustrum/piriform cortex area of the amygdala. Previous studies on the release of CCK from cp have focused on the influence of dopamine agonists. The present study has examined the influence of other neuroactive substances on the release of CCK. The release of CCK from rat cp slices in vitro stimulated by potassium was quantitated with a specific CCK radioimmunoassay. This potassium-stimulated release of CCK was Ca 2+ -dependent. Maximal stimulation of CCK release was observed at 55 mM potassium. Several lines of evidence indicate that the release of CCK from cp is inhibited by some other substance (or substances) released by a Ca 2+ -dependent mechanism from cp along with CCK. Release media from cerebral cortex or cp (called ‘conditioned media’ or CM) inhibits the release of CCK from fresh slices of cp but not from cerebral cortex. The release of dopamine from cp is unaffected by CM from cortex or cp. The identity of the substance in CM which inhibits CCK release from cp is still under investigation, though it appears not to be CCK, dopamine, acetylcholine, somatostatin, leucine enkephalin or γ-aminobutyric acid.
Mutation blocking the specific degradation of reinitiation polypeptides in E. coli.

A NONSENSE mutation in a bacterial gene leads to the synthesis of two kinds of incomplete polypeptides1–4. These are the termination, or T, fragments extending from the normal N terminus to the site of mutation, and the reinitiation, or R, fragments initiating distal to the end of the T fragment and continuing to the normal C terminus. Both the T and the R fragments produced by nonsense mutations in the β-galactosidase gene of Escherichia coli (z gene) are rapidly and selectively degraded in vivo5–7. This contrasts strongly with the wild-type β-galactosidase, which is stable5,7. The degradation of mutant polypeptides implies the existence of proteolytic systems which can distinguish these unstable proteins from the stable ones.
The Costs of Major Wars: The Phoenix Factor

A major unexplored area in the field of international politics is the consequences of major war for members of the international system in terms of power lost or gained. This paper explores these shifts of power among neutrals, winners, and losers as a result of these wars, using a sample of 32 cases and time series analysis. The findings register unexpected but systematic patterns after major conflicts; while winners and neutrals are affected marginally by the conflict, losers' powers are at first eroded. Over the long run (15–20 years), though, the effects of the loss dissipate; losers accelerate their recovery and soon resume antebellum status. It is this phenomenon that the authors call the phoenix factor.
Lysosomal glycogen storage disease with normal acid maltase.

Two unrelated 16-year-old boys had mental retardation, cardiomegaly, and proximal myopathy. One also had hepatomegaly. Histochemistry and electronmicroscopy of muscle biopsies showed lysosomal glycogen storage resembling acid maltase deficiency. Biochemical studies of skeletal muscle showed increased content of glycogen of normal structure; acid a-glucosidase activity in both urine and muscle was normal. Other enzymes of glycogen metabolism were also normal. The cause of this apparently generalized glycogenosis with no demonstrable enzyme defect is unknown.
Insect embryo chromosome techniques.

The whole-mount method for studying chromosomes of insect eggs is used; the eggs are caused to adhere to cover glasses, which are handled in racks especially designed for carrying large numbers. A basic and helpful change in the usual technique after fixation and before staining involves extraction of the material 1 hr to overnight with a 1:1 methanol-chloroform mixture to remove plasmal-reactive substances. Either leucobasic fuchsin or sulfonated azure A after acid hydrolysis may be used satisfactorily to stain the chromosomes.
Precise and in situ genetic humanization of 6 Mb of mouse immunoglobulin genes

Genetic humanization, which involves replacing mouse genes with their human counterparts, can create powerful animal models for the study of human genes and diseases. One important example of genetic humanization involves mice humanized for their Ig genes, allowing for human antibody responses within a mouse background (HumAb mice) and also providing a valuable platform for the generation of fully human antibodies as therapeutics. However, existing HumAb mice do not have fully functional immune systems, perhaps because of the manner in which they were genetically humanized. Heretofore, most genetic humanizations have involved disruption of the endogenous mouse gene with simultaneous introduction of a human transgene at a new and random location (so-called KO-plus-transgenic humanization). More recent efforts have attempted to replace mouse genes with their human counterparts at the same genetic location (in situ humanization), but such efforts involved laborious procedures and were limited in size and precision. We describe a general and efficient method for very large, in situ, and precise genetic humanization using large compound bacterial artificial chromosome–based targeting vectors introduced into mouse ES cells. We applied this method to genetically humanize 3-Mb segments of both the mouse heavy and κ light chain Ig loci, by far the largest genetic humanizations ever described. This paper provides a detailed description of our genetic humanization approach, and the companion paper reports that the humoral immune systems of mice bearing these genetically humanized loci function as efficiently as those of WT mice.
Synthesis, characterization and molecular structures of six-coordinate manganese nitrosyl porphyrins

Manganese(II) porphyrins are isoelectronic with iron(III) porphyrins, and previously reported work suggests that manganese nitrosyl porphyrins are good structural models for their kinetically unstable and biologically relevant ferric–NO analogues. We have prepared a new set of six-coordinate manganese nitrosyl porphyrins of the general form (por)Mn(NO)(L) (por = TTP, T(p-OCH3)PP; L = piperidine, methanol, 1-methylimidazole) in moderate to high yields. The (por)Mn(NO)(pip) complexes were prepared from the reductive nitrosylation of the (por)MnCl compounds with NO in the presence of piperidine. The IR spectra of the (por)Mn(NO)(pip) compounds as KBr pellets show new strong bands at 1746 cm−1 (for TTP) and 1748 cm−1 (for (T(p-OCH3)PP) due to the NO ligands. Attempted crystallization of one of these compounds (por = TTP) from dichloromethane–methanol resulted in the generation of the methanol complex (TTP)Mn(NO)(CH3OH). Reaction of the (por)Mn(NO)(pip) compounds with excess 1-methylimidazole gave the (por)Mn(NO)(1-MeIm) derivatives in good yields. The IR spectra of these compounds show νNO bands that are ∼12 cm−1 lower than those of the (por)Mn(NO)(pip) precursors, indicative of greater Mn→NO π-backdonation in the 1-MeIm derivatives. X-Ray crystal structures of three of these compounds, namely (TTP)Mn(NO)(CH3OH), (TTP)Mn(NO)(1-MeIm) and (T(p-OCH3)PP)Mn(NO)(1-MeIm) were obtained, and reveal that the NO ligands in these complexes are linear.
Bioinformatics and its applications in plant biology.

Bioinformatics plays an essential role in today’s plant science. As the amount of data grows exponentially, there is a parallel growth in the demand for tools and methods in data management, visualization, integration, analysis, modeling, and prediction. At the same time, many researchers in biology are unfamiliar with available bioinformatics methods, tools, and databases, which could lead to missed opportunities or misinterpretation of the information. In this review, we describe some of the key concepts, methods, software packages, and databases used in bioinformatics, with an emphasis on those relevant to plant science. We also cover some fundamental issues related to biological sequence analyses, transcriptome analyses, computational proteomics, computational metabolomics, bio-ontologies, and biological databases. Finally, we explore a few emerging research topics in bioinformatics.
Seed germination of ethylene perception mutants of tomato and Arabidopsis

The involvement of ethylene in determining the time to radicle protrusion was investigated in ethylene-insensitive gain-of-function (GOF) receptor mutants in tomato and Arabidopsis, as well as in single and double loss-of-function (LOF) receptor mutants in Arabidopsis. Because ethylene evolution from seeds is coincident with radicle protrusion, and the ability to convert 1-aminocyclopropane-1-carboxylic acid (ACC) to ethylene is diagnostic for seed vigour, it was hypothesized that ethylene-insensitive mutants would require more time to complete germination compared to wild-type seeds. Mutant Never Ripe (Nr) tomato seeds from two genetic backgrounds refuted this hypothesis, while experiments with wild-type seeds, treated with the ethylene action inhibitors, 2,5-norbornadiene or silver thiosulphate, supported it. However, reciprocal crosses between wild-type and Nr demonstrated that ethylene insensitivity during seed development determined subsequent time to complete germination, rather than the ability of the embryo/endosperm to perceive ethylene in the mature seed during germination. Additionally, seed quality, determined by standard vigour tests, was reduced in Nr compared to wild-type seeds, establishing a disconnection between rapid completion of germination and seed vigour. In Arabidopsis, all ethylene-insensitive GOF, and five of six single LOF mutants, required more time to complete 50% radicle protrusion, while double LOF mutants required the same, or less, time to complete germination compared to wild-type seeds. These findings support a role for ethylene perception in determining the length of time Arabidopsis seeds remain in the lag phase prior to radicle protrusion.
Computation of switch time distributions in stochastic gene regulatory networks

Many gene regulatory networks are modeled at the mesoscopic scale, where chemical populations are assumed to change according a discrete state (jump) Markov process. The chemical master equation (CME) for such a process is typically infinite dimensional and is unlikely to be computationally tractable without further reduction. The recently proposed Finite State Projection (FSP) technique allows for a bulk reduction of the CME while explicitly keeping track of its own approximation error. In previous work, this error has been reduced in order to obtain more accurate CME solutions for many biological examples. In this paper, we show that this "error" has far more significance than simply the distance between the approximate and exact solutions of the CME. In particular, we show that apart from its use as a measure for the quality of approximation, this error term serves as an exact measure of the rate of first transition from one system region to another. We demonstrate how this term may be used to directly determine the statistical distributions for stochastic switch rates, escape times, trajectory periods, and trajectory bifurcations. We illustrate the benefits of this approach to analyze the switching behavior of a stochastic model of Gardner's genetic toggle switch.
A novel Spin Injection Field Effect Transistor

We describe a new Spin Injection Field Effect Transistor (SIFET) with a quasi one-dimensional semiconductor channel and ferromagnetic source/drain contacts. We show that even when the ferromagnetic contacts are non-ideal with less than 100% spin polarization, the spin injection efficiency from the source into the channel can be switched from nearly +100 % to nearly +100 % with a small swing in gate bias at a temperature of 0 K. This corresponds to switching from mostly majority spin injection to mostly minority spin injection at the source end. If the spin polarization in the drain has the same sign as that in the source, then the drain will preferentially transmit injected majority spins while blocking minority spins. Therefore, one can switch the drain current from a maximum value to nearly zero with the gate bias (if there is no spin relaxation in the channel), thereby realizing transistor action. The current modulation and transistor action deteriorate with increasing temperature.
S-Nitrosylation Is Emerging as a Specific and Fundamental Posttranslational Protein Modification: Head-to-Head Comparison with O-Phosphorylation

Nitric oxide (NO) is a free-radical product of mammalian cell metabolism that plays diverse and important roles in the regulation of cell function. Biological actions of NO arise as a direct consequence of chemical reactions between NO or NO-derived species and protein targets. Reactions of NO with transition metals in target proteins have garnered the most attention to date as the principal mechanism of NO signaling; nonetheless, S-nitrosylation of protein Cys residues is rapidly moving to center stage in importance. In general, however, there has been a delay in adequate appreciation of the role of S-nitrosylation in biological signaling by NO. This lag is attributed to a poor understanding of the basis for selective targeting of NO to particular thiols, and methodological limitations in accurately quantifying this modification--recent breakthroughs in concepts and methods diminish these barriers. Here, we consider the wheres and whys of protein S-nitrosylation and its basis for specificity. Protein S-nitrosylation potentially represents a ubiquitous and fundamental mechanism for posttranslational control of protein activity on a par with that of O-phosphorylation.
BENEFITS OF SMALL-SIZED CACHES FOR SCATTER-HOARDING RODENTS: INFLUENCE OF CACHE SIZE, DEPTH, AND SOIL MOISTURE

Some granivorous rodents scatter hoard; they bury seeds in shallow pits throughout their territory. These buried caches can represent food stores for the hoarders, food for competitors, or a means of seed dispersal and propagation for plants. Large numbers of seeds may be buried in many caches throughout an area; thus, fate of caches has important consequences for granivores, other animals, and plants. This study examined the ability of Ord’s kangaroo rat (Dipodomys ordii) to exploit artificial caches of different sizes, at 2 depths, and in substrates of differing moisture content. Kangaroo rats harvested significantly more caches in moist substrates and at shallower depths; however, small caches containing � 5 seeds were removed infrequently by individuals regardless of substrate moisture and depth. As cache size was increased in moist sand, a threshold existed at each depth where caches were greatly exploited by kangaroo rats. Results suggest that pilferage of caches under natural conditions is not linear with respect to cache size in moist substrates. As cache size was increased in dry sand, no threshold of increased exploitation was observed for cache sizes used in this experiment. Results also suggest that pilferage of caches under natural conditions is not strongly influenced by size in dry substrates for relatively small caches. Overall, size and depth of caches greatly influence their fate. Perturbations, such as rainfall, also alter detection of caches. To reduce detection of caches by competitors, scatter hoarders should distribute relatively small caches, especially during wet conditions.
Probing intrinsic charm with semileptonic B decays

We discuss semileptonic B decays of the form B -> J/Psi e nu X as possible probes of intrinsic charm. We calculate the leading order perturbative contribution to the process B- -> J/Psi e- nu_e X and find it to be unobservably small, with a branching ratio ~ 10^-10. We propose a modified spectator model to estimate the intrinsic charm contribution and find that it can be significantly larger, with a branching ratio for B -> (c cbar) e- nu_e X as large as 5 X 10^-7. We show that the process could be observed at these levels by CDF assuming a Run II integrated luminosity of 15 fb^-1, making this a useful reaction to probe the idea of intrinsic charm.
A ray propagation approach for accelerating the fast multipole method

Recently, many researchers have been investigating the use of radiation beam ideas to extend classical integral equation techniques for solution of wave scattering problems into the high frequency regime. Here, we use a "ray" propagation approach to accelerate the fast multipole method (FMM) of Rokhlin. The FMM allows the rapid solution of surface integral equations arising in electromagnetics. In this approach, the integral equation is discretized using, for example, the method of moments (MOM), then solved using an iterative method, such as conjugate gradient. The main bottleneck in the computation is the cost of computing a matrix-vector multiply. A standard matrix-vector multiply for a problem with N unknowns has a cost of O(N/sup 2/). A straight-forward application of the FMM reduces this cost to O(N/sup 3/2/). A two-level nested application further reduces the cost to O(N/sup 4/3/). Here we present a non-nested method, using a ray propagation approach, to reduce the cost of a FMM matrix vector multiply to O(N/sup 4/3/). >
Lichen dating of earthquake-generated regional rockfall events, Southern Alps, New Zealand

Synchronous regional rockfall events triggered by large earthquakes in the Southern Alps of New Zealand were used to evaluate and improve the lichenometry method for surface-exposure dating. Digital calipers were used to measure the maximum diameter of the largest lichen on many rockfall blocks, using a fixed-area largest-lichen (FALL) sampling strategy. Regional significance of FALL peaks can be tested by confirming the occurrence of a coeval peak at multiple sites, and by showing an increase in peak size toward the earthquake epicenter. Significance of FALL peaks at a local site can be described in terms of peak size relative to a uniform density of FALL sizes. Measurements of 34 000 FALL sizes on fully exposed rockfall blocks and outcrop joint faces at 90 sites allow precise dating of geomorphic events of the past 300 to 500 yr. Uncertainties at the 95% confidence interval can be reduced to a level better than ±10 yr for ages within the calibrated time range represented by the lichen growth equation. Recognition of prehistorical regional rockfall events in 1833, 1836, and 1840 demonstrates the excellent resolution of this dating method. Precise dates result from exceptionally low measurement errors of lichen sizes relative to their growth rate, tightly clustered FALL sizes for earthquake-induced rockfall events, and substrate exposure times for calibration sites that are known to the year or day. FALL peaks for synchronous rockfall events are the same for 20 sites with diverse climate, altitude, and substrate lithology. A regionally consistent lichen growth rate allows use of a single growth-rate equation for most species of Rhizocarpon subgenus Rhizocarpon on the South Island of New Zealand. A nonlinear growth equation suggests that the first colonization, on average, occurs in the 5th yr after formation of new rock surfaces (~0.5 m 2 unit areas) and is followed by rapid, exponentially declining growth for about 20 yr (greatgrowth phase) that is largely completed by the 24th yr. Then, linear growth persists at about 15 mm per century (uniform-growth phase).
Myosin regulatory light chain phosphorylation inhibits shortening velocities of skeletal muscle fibers in the presence of the myosin inhibitor blebbistatin

Phosphorylation of skeletal myosin regulatory light chain (RLC) occurs in fatigue and may play a role in the inhibition of shortening velocities observed in vivo. Forces and shortening velocities were measured in permeabilized rabbit psoas fibers with either phosphorylated or dephosphorylated RLCs and in the presence or absence of the myosin inhibitor blebbistatin. Addition of 20 microM blebbistatin decreased tensions by approximately 80% in fibers, independent of phosphorylation. In blebbistatin maximal shortening velocities (V(max)) at 30 degrees C, were decreased by 45% (3.2 +/- 0.34 vs. 5.8 +/- 0.18 lengths/s) in phosphorylated fibers but were not inhibited in dephosphorylated fibers (6.0 +/- 0.30 vs. 5.4 +/- 0.30). In the presence of 20 microM blebbistatin, K(m) for V(max) as a function of [ATP] was lower for phosphorylated fibers than for dephosphorylated fibers (50 +/- 20 vs. 330 +/- 84 microM) indicating that the apparent binding of ATP is stronger in these fibers. Phosphorylation of RLC in situ during fiber preparation or by addition of myosin light chain kinase yielded similar data. RLC phosphorylation inhibited velocity in blebbistatin at both 30 and 10 degrees C, unlike previous reports where RLC phosphorylation only affected shortening velocities at higher temperatures.
Do Patronize Me: The Comparative Political Economy of Arts Patronage, Copyright, and Crowdfunding

Traditional wisdom has long argued that copyright laws are necessary to ensure that expressive works, such as books, music, and films, are produced by deterring people from consuming them for free. Recently, a new method of financing expressive works has emerged, known as crowdfunding, where creators can solicit small contributions from a large number of individual patrons. This provides an opportunity to compare the present system of copyright with other potential complements and alternatives. I construct a simple game-theoretic model to argue that patronage of the arts, where a patron sponsors a creator by paying her fixed costs in exchange for some share of the proceeds and the ability to exclude others, constitutes the basic mechanism of effective expressive work production. In fact, both copyright and crowdfunding are variations of the ancient institution of patronage, only substituting different entities for patrons.
Taxing the Sick: How 'Fees' in Health Care Reform Hurt Patients

The Senate Finance Committee has concluded its consideration of the America's Healthy Future Act of 2009. The legislation intends to address a number of policy objectives, but one overriding concern is controlling the rising cost of health care. As a recent White House report notes, "Americans pay more for health care each year but get less coverage and fewer services for the premiums they pay. . . . With each passing year, families face increasing deductibles, copayments, and other out-of-pocket expenses, requiring them to make difficult decisions in order to make ends meet." It is surprising, therefore, that some of the provisions of this legislation will in fact lead to higher costs for health care consumers.
An exploratory study of concussion management policies in municipal park and recreation departments

ABSTRACTDespite the burgeoning interest in reducing concussions among youth sport participants, research investigating concussion safety policies of municipal park and recreation departments has been sparse. A national survey of park and recreation professionals in 50 states (n = 739, response rate of 23%) was conducted in 2015 to assess concussion management policies and practices of municipal park and recreation departments. Only about one-third of respondents indicated that their departments required coaches to be trained in concussion safety. Among those who mandated concussion safety training, the CDC’s ‘Heads Up: Concussion in Youth Sports’ was the most commonly used concussion safety training material. Despite the low number of departments requiring concussion safety training for youth sport coaches using park/recreation facilities, nearly two-thirds encouraged concussion safety training for such coaches. The results suggest that, overall, municipal park and recreation department’s concussion safet...