cssi/SciSciGPT-SciSciNet huggingface dataset:
Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

Comparative genomics of parasitic protists and their free-living relatives are profoundly impacting our understanding of the regulatory systems involved in transcription and chromatin dynamics. While some parts of these systems are highly conserved, other parts are rapidly evolving, thereby providing the molecular basis for the variety in the regulatory adaptations of eukaryotes. The gross number of specific transcription factors and chromatin proteins are positively correlated with proteome size in eukaryotes. However, the individual types of specific transcription factors show an enormous variety across different eukaryotic lineages. The dominant families of specific transcription factors even differ between sister lineages, and have been shaped by gene loss and lineage-specific expansions. Recognition of this principle has helped in identifying the hitherto unknown, major specific transcription factors of several parasites, such as apicomplexans, Entamoeba histolytica, Trichomonas vaginalis, Phytophthora and ciliates. Comparative analysis of predicted chromatin proteins from protists allows reconstruction of the early evolutionary history of histone and DNA modification, nucleosome assembly and chromatin-remodeling systems. Many key catalytic, peptide-binding and DNA-binding domains in these systems ultimately had bacterial precursors, but were put together into distinctive regulatory complexes that are unique to the eukaryotes. In the case of histone methylases, histone demethylases and SWI2/SNF2 ATPases, proliferation of paralogous families followed by acquisition of novel domain architectures, seem to have played a major role in producing a diverse set of enzymes that create and respond to an epigenetic code of modified histones. The diversification of histone acetylases and DNA methylases appears to have proceeded via repeated emergence of new versions, most probably via transfers from bacteria to different eukaryotic lineages, again resulting in lineage-specific diversity in epigenetic signals. Even though the key histone modifications are universal to eukaryotes, domain architectures of proteins binding post-translationally modified-histones vary considerably across eukaryotes. This indicates that the histone code might be "interpreted" differently from model organisms in parasitic protists and their relatives. The complexity of domain architectures of chromatin proteins appears to have increased during eukaryotic evolution. Thus, Trichomonas, Giardia, Naegleria and kinetoplastids have relatively simple domain architectures, whereas apicomplexans and oomycetes have more complex architectures. RNA-dependent post-transcriptional silencing systems, which interact with chromatin-level regulatory systems, show considerable variability across parasitic protists, with complete loss in many apicomplexans and partial loss in Trichomonas vaginalis. This evolutionary synthesis offers a robust scaffold for future investigation of transcription and chromatin structure in parasitic protists.
Improved Surgical Technique for the Establishment of a Murine Model of Aortic Transplantation

Aortic allotransplantation is a reliable procedure to study the evolvement of chronic rejection in mice. The progressive nature of this process in mice is characterized by diffuse and concentric myointimal proliferation which is inevitably associated with variable degrees of luminal constriction. These vascular changes are comparable to those that are witnessed in organ allografts undergoing chronic rejection in humans, underscoring its utility as a model of choice for the study of the development of this lesion. Whilst improved surgical technique has resulted in markedly enhanced graft survival, the results are far from being acceptable. Realizing this limitation, we embarked on developing a modified technique for aortic transplantation which would allow for improved graft survival in mice. A bypass conduit was created by end-to-side anastomosis of a segment of the donor's thoracic aorta into the infrarenal portion of the recipient's abdominal aorta. Using this technique, the graft survival was >98% with evidence in allotransplanted aorta of morphological changes pathognomonic of chronic rejection. On the contrary, no histopathological anomalies were discerned in aortic grafts transplanted across syngeneic animals. This modified surgical approach ameliorates the unacceptably high graft loss associated with earlier techniques, further extending the utility of this model as a tool to study the molecular and cellular mechanisms rudiment to the evolvement of chronic rejection.
Protecting the Sanctity of Native Foods

Indigenous peoples are the caretakers of many of the last biodiverse places on Earth. Even though they only constitute 5 percent of world population and occupy 20 percent of the earth’s surface, they live in 80 percent of the world’s biological diversity hotspots. They are therefore critical to ecosystem health and should be recognized as major stakeholders and leaders in the global sustainability movement.1
Water is Not H2O

In this essay I have discussed an assumption of semantic externalist theories which I called the coordination principle. This is the idea that natural language kinds and scientific kinds line up or can be mapped onto one another one-to-one. A closer look at water shows that there is not this type of simple one-to-one match between chemical and ordinary language kinds. In fact, the use of kind terms in chemistry is often context sensitive and in cases where chemists want to ensure no ambiguity, they use a very complex and nuanced set of kind terms, none of which could be reasonably associated with the ordinary language kind term “water” alone. Since we cannot just turn to chemistry to find a single chemical kind that can be used to determine the extension of “water,” there is not any strict sense in which water is H2O, because exactly what water is depends on the context in which “water” is uttered.
Trade Liberalization vs. Agricultural Import Restriction

Under section 22 of the Agricultural Adjustment Act the President has since 1935 had authority to impose quotas or fees upon agricultural imports if these imports were believed to be adversely affecting United States farm price and income support programs. Notwithstanding urgent demands from commodity interest groups to invoke this authority it has been used only on a few commodities. Constraints upon use have come mainly from two sources: lack of evidence that imports were adversely affecting domestic programs, and diplomatic interests. Nevertheless in its potential and actual use this authority has had a substantial trade inhibiting effect. Since the Trade Expansion Act of 1962 has ample general provisions to protect domestic groups and industries, the authors conclude that the special provisions of section 22 should be terminated and that the general provisions of the 1962 act should be utilized as justified for farm products. Termination of section 22 should improve the posture of the United States for obtaining concessions in counterpart restrictive devices applied against our farm exports, including EEC's variable import levy.
NMR Detection of New Hydrogen Populations in Amorphous and Crystalline Silicon

Deuteron magnetic resonance (DMR) has been used to further examine hydrogen (deuteron) populations in amorphous-silicon (a-Si) and in n-type crystalline silicon (x-Si). In both a-Si and x-Si DMR shows central components arising at least in part from isolated molecular deuterium and sharp doublet features from Si-bonded hydrogen (D). Our new results include the observation in x-Si of molecule-specific DMR multiple echoes from trapped ortho-D2. A second new result is the observation in x-Si of a substantialn Si-bonded D population with splittings between 46 and 80 kHz and perhaps arising from (deuterated) hydrogen bond-centered and antibonding configurations.
Lymphopenia and the secretion of adrenalin.

SummaryHemorrhage (1 cc/100 g body weight) and general excitement (induced by the action of a subconvulsive electrical shock) cause lymphopenia and relative neutrophilia in normal but not in adrenodemedullated rats. Insulin hypoglycemia leading to coma induces a greater lymphopenia in normal than in adrenodemedullated animals. It is concluded that hemorrhage, general excitement and insulin coma cause an increased secretion of adrenalin followed by an increased discharge of adrenocortical hormones. Hypoglycemia seems to induce some increased adrenocortical secretion even in the absence of the adrenal medulla.
In situ observation of water behavior at the surface and buried interface of a low-k dielectric film.

Water adsorption in porous low-k dielectrics has become a significant challenge for both back-end-of-line integration and reliability. A simple method is proposed here to achieve in situ observation of water structure and water-induced structure changes at the poly(methyl silsesquioxane) (PMSQ) surface and the PMSQ/solid buried interface at the molecular level by combining sum frequency generation (SFG) vibrational spectroscopic and Fourier transform infrared (FTIR) spectroscopic studies. First, in situ SFG investigations of water uptake were performed to provide direct evidence that water diffuses predominantly along the PMSQ/solid interface rather than through the bulk. Furthermore, SFG experiments were conducted at the PMSQ/water interface to simulate water behavior at the pore inner surfaces for porous low-k materials. Water molecules were found to form strong hydrogen bonds at the PMSQ surface, while weak hydrogen bonding was observed in the bulk. However, both strongly and weakly hydrogen bonded wat...
Self-assembly of Silicon Nanotubes

The growth of silicon nanotubes (SiNTs) by a dual-RF-plasma treatment technique is reported here. These SiNTs are vertically aligned and self-assembled from Si substrates at 500 °C by the use of Cu catalysts. Their diameters are ~50 to 80 nm with tubular wall thickness of ~10–15nm. Cu vapors were found partially filled inside the SiNTs. This is a novel technique that can convert bulk materials into their nanostructures.
Reply to Levermann et al.: Linear scaling for monsoons based on well-verified balance between adiabatic cooling and latent heat release

We showed (1) that an analytical model of monsoons exhibits no abrupt response to forcing changes when one assumes, consistent with observations (2), that monsoon circulations export energy away from their ascending branch. We claimed that a previous model (3) incorrectly produced an abrupt response because it neglected the adiabatic cooling of rising air in a stably stratified troposphere. Levermann et al. argue (4) that the abrupt response is preserved in the ref. 3 model as long as adiabatic cooling does not balance the latent heat released during precipitation formation, and that neither theory nor observations support the idea that “most of the energy from the rain’s latent … [↵][1]1To whom correspondence should be addressed. Email: billboos{at}alum.mit.edu. [1]: #xref-corresp-1-1
Misconceptions about the ability of researchers to relocate the holotype of the Galapagos pink land iguana through the use of a passive integrated transponder

Isla Isabela is the largest island in the Galapagos archipelago and hosts three endemic iguanid lizard species (Tzika et al. 2008, Gentile & Snell 2009): Amblyrhynchus cristatus (Bell, 1825), Conolophus subcristatus (Gray, 1831) and Conolophus marthae Gentile & Snell, 2009. The first iguanid listed exists as a marine species and the latter two are restricted to the terrestrial environment. It should be noted, however, that all three species can hybridize and produce viable offspring (Tzika et al. 2008). The International Union for Conservation of Nature (IUCN) lists the marine iguana A . cristatus as a “threatened” species and the land iguana species C . subcristatus as “vulnerable”. Currently there are no studies that assess the status of the iguana C . marthae , so its status is given as “not evaluated” by the IUCN.
TOWARDS DETERMINATION OF THE THREONINE REQUIREMENT OF YEARLING HORSES FED VARYING DIETARY COMPOSITIONS USING THE INDICATOR AMINO ACID OXIDATION METHOD

OF THESIS DETERMINATION OF THE THREONINE REQUIREMENT OF YEARLING HORSES FED VARYING DIETARY COMPOSITIONS USING THE INDICATOR AMINO ACID OXIDATION METHOD The amino acid requirements of growing horses are currently unknown, and studies suggest that threonine is a limiting amino acid in common horse diets. Thus, the objective of this study was to determine the threonine requirement of growing horses fed two different forage to concentrate ratios using the indicator amino acid oxidation (IAAO) method. The study consisted of a high concentrate phase (HC; 60% concentrate and 40% forage) and a high forage phase (HF; 25% concentrate and 75% forage). Within each phase, 6 yearling horses were randomly assigned each of 6 dietary treatments in a 6 x 6 Latin square design. All 6 treatments were identical, apart from varying equimolar ratios of threonine to glutamate. After 6 days of adaptation, blood samples were collected for plasma urea nitrogen (PUN) and amino acid analysis. On day 7, horses underwent the IAAO protocol, during which regular breath and blood samples were collected. Phenylalanine flux, oxidation, non-oxidative disposal, and release from body protein, as well as total carbon dioxide production were calculated using plateau enrichment of samples. There was a significant linear effect of threonine intake on plasma threonine concentrations, and PUN had a significant linear response during the HC phase. There was no significant effect of treatment on phenylalanine oxidation during either phase (P ≥ 0.05). It is unlikely that threonine was limiting in the experimental diets.
The normal and pathologic anatomy of the transversus abdominis muscle in inguinal and femoral hernia.

Restoration of the continuity of the transversus abdominis layer should be the primary objective of the hernia operation. The normal anatomy of this layer is presented, and the defects that permit the development of the three types of groin hernias are described and illustrated.
Two decades of genetic consistency in a reproductive population in the face of exploitation: patterns of adult and larval walleye (Sander vitreus) from Lake Erie’s Maumee River

Analyses of genetic variability and allelic composition in a species exhibiting reproductive fidelity to natal sites may provide important ecological indication of temporal population dynamics, facilitating understanding responses to past disturbances and future climate change. The walleye is an ecologically and economically valuable species, whose largest fishery centers in Lake Erie of the Laurentian Great Lakes; it exhibits reproductive site fidelity, despite otherwise wide-ranging dispersal. We tested whether genetic composition and diversity have remained temporally stable in Lake Erie’s Maumee River, which is the largest and most highly fished spawning run. This population has experienced over a century of exploitation, habitat alterations, and pollution, which may have affected genetic structure and might influence future sustainability. Fourteen nuclear DNA microsatellite loci were analyzed from 744 spawning run walleye to test genetic patterns across: (1) years (N = 12, spanning 1995–2013), (2) birth year cohorts, (3) the sexes, (4) those reproducing earlier (ages 2–6) versus later (7 or older) in life, and (5) the adults versus larvae. Results indicated stability in genetic diversity levels (mean H O = 0.76 ± 0.03) and allelic composition across years (F ST = 0.000–0.006, NS), cohorts (F ST = 0.000–0.013, NS), sexes (F ST = 0.000, NS), earlier versus later reproduction (F ST = 0.000, NS), and between the larvae and adults (F ST = 0.000–0.004, NS). Number of breeders and effective population size were substantial and consistent. This reproductive population thus has maintained genetic stability and high diversity, despite intensive anthropogenic pressures.
239. Induction of Allograft Immune Tolerance with Bioengineered Thymus Organoids

One of the major obstacles in solid organ transplantation is to establish immune tolerance of allografts. While immunosuppressive drugs can prevent graft rejection to a certain degree, their efficacies are limited, impermanent, and associated with severe side effects. As a primary immune organ essential to adaptive immunity, the thymus continuously generates a diverse population of naive T-cells, which can effectively react to invading pathogens, but remains unresponsive to self-antigens. Many factors (e.g. infection, irradiation, drug treatments, or aging) can irreversibly compromise thymic function, resulting in immune deficiency, cancer, autoimmunity and other immunodysregulatory diseases. While numerous efforts have been made to modulate/rejuvenate thymic function, manipulating the thymus, either in vitro or in vivo, proves to be difficult. The major challenge is to reproduce its unique extracellular matrix microenvironment that is critical for the survival and function of thymic epithelial cells (TECs). TECs are the predominant population of thymic stromal cells that are essential for T-cell lineage determination and maturation. TECs cultured in the traditional 2-D culture rapidly lose their molecular properties and fail to grow, which prohibits them from undergoing genetic modification. We have recently developed a thymus decellularization technique, which allows us to reconstruct a functional thymus organoid de novo with isolated TECs. The 3-D thymic scaffolds can support the survival of TECs in vitro, and maintain their unique molecular properties. When transplanted into athymic nude mice, the bioengineered thymus organoids could effectively promote the homing of lymphocyte progenitors and support the development of a diverse, self-tolerant T-cell repertoire. The thymus-reconstructed nude mice could promptly reject skin allografts, and were able to mount antigen-specific humoral responses against ovalbumin upon immunization. Notably, tolerance to allogeneic skin grafts could be achieved by transplanting thymus organoids constructed with either TECs co-expressing both syngeneic and allogenic MHCs, or mixtures of donor and recipient TECs. Our results demonstrate the technical feasibility of inducing donor-specific allogeneic tolerance with bioengineered thymus organoids and highlight the clinical implications of this thymus reconstruction technique in solid organ transplantation and regenerative medicine.
Empirical study of students' perceptions of online courses

The recent proliferation of availability of online courses and programs has caused some concerns related to ensuring that the time and cost investments provide beneficial results, both to students and the institutions providing the material. Students' perceptions of these programs are likely to affect their interest in enrolling in them. Schools need an awareness of these student perceptions to determine if a need exists to modify the delivery of online programs. This study was designed to determine current perceptions of online programs by potential students, compared with the traditional on-campus environment. Findings indicate those issues that are most important to students in course delivery and their beliefs as to whether these issues are more likely to be delivered through online or through traditional on-campus courses.
Retention and effects of miniature transmitters in juvenile American eels

Abstract The purpose of this study was to assess the effects of an acoustic micro transmitter (tag) on survival and swimming ability of juvenile American eels (Anguilla rostrata). The transmitter was designed for implantation through a
External Genital Development, Urethra Formation, and Hypospadias Induction in Guinea Pig: A Double Zipper Model for Human Urethral Development.

Objective To determine whether the guinea pig phallus would be an appropriate model of human penile development, we characterized the embryology and sexual differentiation of guinea pig external genitalia and attended to induce hypospadias in males and tubular urethra formation in females pharmacologically. Materials and Methods The external genitalia of guinea pig were collected from genital swelling initiation to newborn stages, and scanning electronic microscopy and histology were performed to visualize the morphology and structure. Immunohistochemistry was used to determine the androgen receptor localization. Bicalutamide and methyltestosterone were given to pregnant dams to reveal the role and timing of androgen in guinea pig penile masculinization. Results Canalization and dorsal-to-ventral movement of the urethral canal develops the urethral groove in both sexes, and then the males perform distal-opening-proximal-closing to form tubular urethra. More nuclear-localized androgen receptor is found in proximal genital tubercles of males than in females at (E) 29. Antiandrogen treatment at E26-E30 can cause hypospadias, and methyltestosterone administration at E27-E31 can induce tubular urethra formation in females. Conclusion Fetal development of the guinea pig phallus is homologous to that of humans. Although guinea pig has structures similar to mouse, the urethral groove and the tubular urethra formation are more similar to humans. Antiandrogen treatment causes hypospadias in males and additional androgen induces tubular urethra formation in females. Thus, guinea pig is an appropriate model for further study of cellular and molecular mechanisms involved in distal-opening-proximal-closing in tubular urethra formation and the evaluation of the pathophysiological processes of hypospadias.
Autor, editor e editado: Erico Verissimo sob o crivo norte-americano

This article examines some of the complexities involved in the intercultural transit of books and politics of translation. Supported by archival research and focusing on the international career of Brazilian writer Erico Verissimo, the paper outlines the publishing process of Verissimo’s works in the United States and reveals various responses they drew from editors, translators, and free-lancer readers. I argue that the trajectory of Verissimo’s editions in the United States sheds light on publishing procedures, editorial expectations, and cultural filters that impact the screening of foreign literature and the selection of titles for translation.
The Emergent Nature of Ethnicity: Dilemmas in Assessment:

Clinical use of a traditional culture paradigm for ethnic assessment is widespread. However, as interest in ethnicity has increased, investigators have been less able to document the emergent natur...
Genetic and environmental factors affecting drug disposition in man

Large interindividual variations in drug response can arise from multiple genetic and environmental factors affecting drug absorption, distribution, biotransformation, excretion, interaction with receptor sites, or combinations of these. Twin and family studies disclosed that for several commonly used drugs genetic factors are predominantly responsible for large interindividual variations in drug disposition that occur in normal volunteers under basal conditions. Environmental contributions were surprisingly small. While it has been convenient in such studies to separate genetic from environmental contributions as though they were discrete, unrelated entities, the transcriptional and translational mechanisms by which genetic information is expressed require environmental participation. Conversely, many environmental factors that alter rates of drug disposition do so by affecting genetic mechanisms (for example, phenobarbital induction of human hepatic antipyrine metabolism and benzpyrene induction of aryl hydrocarbon hydroxylase [AHH] activity in cultured human lymphocytes). Environmental chemicals, such as DDT, polychlorinated biphenyls, and polycyclic hydrocarbons, can alter, through induction, basal, genetically controlled hepatic drug-metabolizing enzyme activity. Disease states can markedly change an individual's basal, genetically controlled rate of drug elimination. Assurance of a truly basal, uninduced, or uninhibited state can never be complete but is partially attainable through repeated measurements of the rate of elimination of a particular drug and through a careful history of exposures at work and at home to potential compounds or conditions that could alter the basal rate of drug elimination. The existence and operation of numerous environmental factors, each with differing capability of altering the basal, genetically controlled level of drug metabolism, make it exceedingly difficult to attribute quantitatively different portions of the total interindividual variation to specific single environmental factors. In this regard, a major problem in man is that most populations are markedly heterogeneous with respect both to environmental and genetic factors that influence drug disposition. The task of partitioning the total interindividual variation in drug elimination of such heterogeneous populations into component parts is further complicated because some seemingly pure “environmental” factors (smoking and diet) are closely associated with other
A summary of selected US basecourse specifications

Unbound aggregate bases are commonly used in the United States. Each of the 50 state transportation agencies has developed their own material and construction specifications which in many instances vary considerably. Specifications are briefly summarized for eight typical states having widely varying climates and materials. Density, gradation, durability, placement and construction tolerances are included in the discussion.
Method for Precision Nitrogen Management in Spring Wheat: II. Implementation

By accounting for spatial variation in soil N levels, variable-rate fertilizer application may improve crop yield and quality, and N use efficiency within fields. The main purpose of this study was to demonstrate how site-specific wheat yield and protein data, and a geographic information system may be used in developing precision N-recommendations for spring wheat. The three steps in the procedure include: (1) estimate the amount of N-removed in wheat in the year in which the crop is harvested, (2) estimate the N-deficit, defined as the amount of additional N needed for raising protein concentration in a future crop to a specified target level, and (3) estimate the total N-recommendation by summing the mapped values of the N-removed and the N-deficit. A map for variable-rate application of fertilizer is derived by specifying cutoff values to divide the range in the total N-recommendation into classes representing N management zones. A field experiment was conducted within an annually cropped wheat field (101 ha) in northern Montana to determine whether the proposed method could improve grain yields and protein levels. The N-removal and N-deficit were estimated from site-specific wheat yield and protein data that were acquired during harvest of 1996. In 1997, which was a dry year, an experiment was conducted in the same field that consisted of a randomized complete block design arranged as pairs of strip plots. Variable- or uniform-rate N treatments were randomly assigned to each pair of strips. Both treatments received nearly the same amount of fertilizer, however, N in the variable treatment was varied to match patterns in grain yield and protein levels that previously existed in 1996. Yields were not significantly different between management systems, but proteins were significantly enhanced by spatially variable N application. In addition, variability in protein levels was reduced within the whole field. Field areas deficient in N fertility could be identified without having to sample for soil profile N.
Endoscopic ultrasound guided fine needle aspiration of the pancreas.

Currently, pancreatic cancer is the fourth leading cause of cancer-associated deaths in the United States and ranks ninth in its incidence. Increased mortality from this tumor results from multiple factors including detection at advanced stages, aggressive biology, and relative resistance to available therapy. It is reported that resection of early (size<3.0cm) organ-confined tumors provide significantly improved patient survival in comparison to large tumors.1 It is, therefore, important to detect these tumors early. Imaging studies (percutaneous ultrasound and CT scan) have provided a valuable support in detection of these tumors for a long time. Endoscopic ultrasound (EUS) is a relatively new imaging modality and is reported to be superior to both CT scans and MRI in detecting pancreatic lesions, especially when lesions are smaller than 3.0 cm.2
Mechanical Behavior and Deformation Mechanisms of Mg-based Alloys in Shear Using In-Situ Synchrotron Radiation X-Ray Diffraction

A fundamental understanding of magnesium-based alloys during high rate, large deformation processes that occur during impact and penetration are not well-known. This metal possesses a limited number of deformation mechanisms, each with their own disparate strengths, strain hardening rates, and strain rate sensitivities. Consequently, these alloys exhibit severe tension-compression asymmetry and anisotropy dictated by their processing history and the applied deformation. Thus, an understanding of material behavior undergoing large shears at dynamic rates is required. Experiments have been performed on a specimen geometry that induces shear localization in “pure” simple shear, called the compact forced simple shear (CFSS) specimen. The deformation occurs on a 2D plane in the specimen, which is oriented with respect to directional aspects of the material’s microstructure and deformation modes. Experiments at dynamic strain rates have been performed to determine how the mechanical behavior in shear evolves and correlates to the microstructural deformation mechanisms. The experiments were performed at the Dynamic Compression Sector of the Advanced Photon Source at Argonne National Laboratories using in-situ synchrotron x-ray diffraction aimed to probe the microstructural evolution during shear-induced localization. By correlating the propensity for shear localization to occur with the mechanical response of various orientations, we have built a data set to compare existing models to identify key deformation mechanisms responsible for localization.
Competitive Intramolecular Amination as a Clock for Iron-Catalyzed Nitrene Transfer

Reaction of the complex [(TpPh,Me)FeII(NCMe)3]BF4, where TpPh,Me = hydrotris(3-phenyl,5-methyl-1-pyrazolyl)borate, with the iodonium heteroylide PhI═NTs (1.5 equiv) is proposed to result in the insertion of N-tosylnitrene into one C–H bond at the ortho ring position of a 3-pyrazole phenyl substituent; subsequent deprotonation of the nascent aniline and one-electron oxidation of iron forms TsNH2 (0.5 equiv) as a coproduct. The covalent ligand modification and oxidation results in an intense purple-brown anilinato–iron(III) LMCT chromophore. This intramolecular reaction is utilized as a consistent clock to determine relative rates of competitive intermolecular nitrene transfer to added substrates, specifically to para-substituted styrenes and thioanisoles. Prior addition of substrate to the reaction of PhI═NTs with the iron(II) complex attenuates the CT absorbance of the equilibrium solution. Fitting of the concentration-dependent absorption data gives the ratio of intra- versus intermolecular nitrene trans...
Transanal proximal rectosigmoidectomy. A new operation for severe chronic idiopathic constipation associated with megarectosigmoid.

Abstract Background At the severe end of the idiopathic constipation spectrum exist patients with chronic idiopathic constipation associated with an enormous megarectosigmoid, among whom few require surgery. We performed transanal proximal rectosigmoidectomy, involving preservation of a 5 cm rectal reservoir, to ameliorate inconsistent and unpredictable outcomes and fecal incontinence occurring in some patients operated on with other techniques. Methods We retrospectively observed patients with chronic idiopathic constipation with megarectosigmoid who underwent transanal proximal rectosigmoidectomy during July 2017–May 2018. We analyzed sex, age, operation indication, complications, functional outcome, and time of follow-up. We statistically compared the dosage of laxative before and after the procedure. Results Thirteen patients were included in the study. Median age during surgery was 8 years. In 9 cases, the indication for surgery was chronic intake of a daily high dose of Senna with failed weaning trials, and 4 had persistent fecal impaction with laxative-intolerance and refusal of rectal enemas. No intra/postoperative complications occurred. Currently, all 13 patients have daily voluntary bowel movements and no fecal accidents. Laxative dosage was significantly reduced (p = 0.007). Follow-up ranged 6–16 months. Conclusion Preliminary results suggest transanal proximal rectosigmoidectomy as an adequate alternative for patients requiring surgery for chronic idiopathic constipation with megarectosigmoid. Type of study Clinical research. Level of evidence Level III.
Social–Spatial Analyses of Attitudes toward the Desert in a Southwestern U.S. City

Land change due to urbanization often results in the loss of desert ecosystems. The loss of desert land affects ecological and social processes in arid cities, such as habitat provisioning, the ext...
The Schrödinger operator with Morse potential on the right half-line

This paper studies the Schrodinger operator with Morse potential Vk(u) = 1 e 2u + ke u on a right half-line (u0, ∞), and determines the Weyl asymptotics of eigenvalues for con- stant boundary conditions at the endpoint u0. In consequence it obtains information on the location of zeros of the Whittaker function Wκ,� (x), for fixed real parameters κ, x with x > 0, viewed as an entire function of the complex variable � . In this case all zeros lie on the imaginary axis, with the possible exception, if κ > 0, of a finite num- ber of real zeros which lie in the interval −κ < � < κ . We obtain an asymptotic for- mula for the number of zeros N(T) = {ρ | Wκ,ρ(x) = 0, |Im(ρ)| < T } of the form N(T) = 2 T log T + 2 (2log 2 − 1 − log x)T + O(1). Parallels are observed with zeros of the Riemann zeta function.
Early antibiotics use in young infants with invasive bacterial infection visiting emergency department, a single medical center's experience.

Background The Surviving Sepsis Campaign (SSC) recommends that intravenous antimicrobials be administered within one hour to treat sepsis in both adult and pediatric patients. However, most studies on the timing of antibiotics have been based on adults so far. Therefore, the goal of this study was to clarify the clinical outcomes of the timing of antibiotics use in young infants diagnosed with invasive bacterial infections. Methods We conducted this retrospective, cohort study at a single tertiary medical center during the period of 2007–2013 and included young infants visiting the PED diagnosed with an invasive bacterial infection. Early antibiotics use is defined as broad-spectrum intravenous antibiotics given within one hour of a patient's triage at PED. In this study, we have analyzed the factors associated with early antibiotics use and measured such primary outcomes as mortality, ICU admission, ventilation support, and length of hospital stay. Results A total of 1231 visits of young infants with fever occurred during our study period, and we included 41 patients in our study; 29 of them were diagnosed with bacteremia and the remaining 12 with bacterial meningitis. Early antibiotics use was also associated with a shortened hospital stay (14 ± 8.5 vs. 24 ± 19.6; p = 0.043). However, no statistical differences were observed with regard to mortality, ICU admission, or ventilation support. Conclusion Among young infants that visited the pediatric department with an invasive bacterial infection, early broad-spectrum antibiotics use was not associated with reduced mortality rate, ICU admission, or ventilator support. However, it may have advantages regarding hospital length of stay.
Cross-National Comparisons of Inequality and Poverty Position

The distribution of income, or of economic well-being, between rich and poor, and the relative position of various groups in the income size distribution has been an important economic and policy issue for quite some time. This chapter illustrates the usefulness of a database such as Luxembourg Income Study (LIS) for cross-national comparisons of inequality and poverty. It provides the nuts and bolts of LIS: its basic structural elements and design. The chapter demonstrates the flexibility of LIS by setting the stage for comparisons of several measures of inequality, poverty and relative income position across the ten countries which comprise the LIS database. The middle-class and well-to-do income levels are designed to show where the population that is neither poor nor at risk of becoming poor is situated in the income spectrum. These categories are important to the budgetary realities of a modern welfare state because growing demands on public entitlements may require either increased taxes or benefit reductions.
Short-Term Radiographic Evaluation of a Tri-Tapered Femoral Stem in Direct Anterior Total Hip Arthroplasty.

Introduction Direct anterior approach (DAA) total hip arthroplasty (THA) has become increasingly popular, largely due to utilization of a true internervous and intermuscular plane. However, recent literature has demonstrated an increased rate of femoral implant subsidence with this approach. Hence, different femoral implants, such as the tri-tapered femoral stem, have been developed to facilitate proper component insertion and positioning to prevent this femoral subsidence. The purpose of this study was to evaluate the subsidence rate of a tri-tapered femoral stem implanted utilizing a DAA, and to determine if the proximal femoral bone quality affects the rate of subsidence. Methods A retrospective analysis of 155 consecutive primary THAs performed by a single surgeon was conducted. Age, gender, primary diagnosis, and radiographic measurements of each subject were recorded. Radiological evaluations, such as bone quality, femoral canal fill, and implant subsidence, were measured on standardized anteroposterior (AP) and frog-leg lateral radiographs of the hip at 6-week and 6-month postoperative follow-up evaluations. Results The average subsidence of femoral stems was 1.18 ± 0.8 mm. There was no statistical difference in the amount of subsidence based on diagnosis or proximal femora quality. The tri-tapered stem design consistently filled the proximal canal with an average of 91.9 ± 4.9% fill. Subsidence was not significantly associated with age, canal flare index (CFI), or experience of the surgeon. Conclusion THA utilizing the DAA with a tri-tapered femoral stem can achieve consistent and reliable fit regardless of proximal femoral bone quality.
Connectome subgraph isomorphisms and graph queries with DotMotif

As connectomics datasets continue to grow in size and complexity, methods to search for and identify interesting graph patterns offer a promising approach to quickly reduce data dimensionality and enable discovery. Recent advances in neuroscience have enabled brain structure exploration at the level of individual synaptic connections. These graphs are often too large to be analyzed manually, presenting significant barriers to searching for structure and testing hypotheses. We combine graph database and analysis libraries with an easy-to-use neuroscience grammar suitable for rapidly constructing queries and searching for subgraphs and patterns of interest. This abstracts many of the computer science and graph theory challenges associated with nanoscale brain network analysis and allows scientists to quickly achieve reproducible findings at scale. We demonstrate these tools to search for motifs on simulated data and real public connectomics datasets, and share simple and complex structures relevant to the neuroscience community. We contextualize these results and provide case studies to motivate future neuroscience questions. All of our tools are released open source to empower other scientists to use and extend these methods.
The condition-care scale: A practical approach to monitoring progress in vacant lot stewardship programs

Abstract Condition and care are key expressions of landscape stewardship and are especially important in managing vacant urban lands. In this context, visible signs of stewardship have been associated with increased neighborhood sense of place whereas signs of physical disorder reflect perceived and actual crime. To date, assessments of condition/care and disorder using neighborhood audits have shown good reliability in field and virtual assessments but are often labor-intensive, particularly when repeated over time or applied across multiple study areas. Integrating the research traditions of neighborhood audits and visual landscape quality assessment, we propose an alternative approach, the “condition-care scale,” and pilot test this seven-point rating scale to assess longitudinal and cross-sectional patterns of stewardship in response to a vacant land reuse program. Lots purchased by nearby residents through the Chicago Large Lot Program were rated on the scale using Google Street View imagery, field photography, and field visits in 2014 (before purchase), 2015, 2016, and 2018 (1–4 years after purchase). Lab and field assessments showed strong intra- and inter-rater scale reliability, and independent measures of lot condition and care from parallel visual and social assessments support the scale’s validity. Longitudinal analyses showed that the greatest improvements were made in the first year after purchase but that improvement levels increased steadily over five years. Cross-sectional comparisons showed significant differences between some community areas. We discuss the utility of our approach for evaluating progress in vacant land reuse programs and its generalizability to other needs of urban greening professionals.
Clinical informatics subspecialists: characterizing a novel evolving workforce.

Background The growing complexity of data systems in health care has precipitated increasing demand for clinical informatics subspecialists. The first board certification exam for the clinical informatics subspecialty was offered in 2013. Characterizing trends in this novel workforce is important to inform its development. Methods We conducted an exploratory analysis of American Board of Medical Specialties data on individuals certified in clinical informatics from 2013 to 2019 to review trends and demographic characteristics of current subspecialists. Results 2018 physicians were certified in clinical informatics from 2013 to 2019. The annual number of awarded certifications declined after 2016. The majority of primary certifications held by clinical informaticians were in broad-based medical specialties relative to primarily procedural specialties. Conclusions Disparities may exist within the clinical informatics physician workforce with respect to primary specialty certifications and geographic distribution. There remains a need for the creation of fellowship programs to sustain the growth of this workforce.
The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array

Abstract Linker histones bind to nucleosomes and modify chromatin structure and dynamics as a means of epigenetic regulation. Biophysical studies have shown that chromatin fibers can adopt a plethora of conformations with varying levels of compaction. Linker histone condensation, and its specific binding disposition, has been associated with directly tuning this ensemble of states. However, the atomistic dynamics and quantification of this mechanism remains poorly understood. Here, we present molecular dynamics simulations of octa-nucleosome arrays, based on a cryo-EM structure of the 30-nm chromatin fiber, with and without the globular domains of the H1 linker histone to determine how they influence fiber structures and dynamics. Results show that when bound, linker histones inhibit DNA flexibility and stabilize repeating tetra-nucleosomal units, giving rise to increased chromatin compaction. Furthermore, upon the removal of H1, there is a significant destabilization of this compact structure as the fiber adopts less strained and untwisted states. Interestingly, linker DNA sampling in the octa-nucleosome is exaggerated compared to its mono-nucleosome counterparts, suggesting that chromatin architecture plays a significant role in DNA strain even in the absence of linker histones. Moreover, H1-bound states are shown to have increased stiffness within tetra-nucleosomes, but not between them. This increased stiffness leads to stronger long-range correlations within the fiber, which may result in the propagation of epigenetic signals over longer spatial ranges. These simulations highlight the effects of linker histone binding on the internal dynamics and global structure of poly-nucleosome arrays, while providing physical insight into a mechanism of chromatin compaction. Significance Linker histones dynamically bind to DNA in chromatin fibers and serve as epigentic regulators. However, the extent to which they influence the gamut of chromatin architecture is still not well understood. Using molecular dynamics simulations, we studied compact octa-nucleosome arrays with and without the H1 linker histone to better understand the mechanisms dictating the structure of the chromatin fiber. Inclusion of H1 results in stabilization of the compact chromatin structure, while its removal results in a major conformational change towards an untwisted ladder-like state. The increased rigidity and correlations within the H1-bound array suggests that H1-saturated chromatin fibers are better suited to transferring long-range epigentic information.
scFEA: A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data

ABSTRACT The metabolic heterogeneity, and metabolic interplay between cells and their microenvironment have been known as significant contributors to disease treatment resistance. However, with the lack of a mature high-throughput single cell metabolomics technology, we are yet to establish systematic understanding of intra-tissue metabolic heterogeneity and cooperation phenomena among cell populations. To mitigate this knowledge gap, we developed a novel computational method, namely scFEA (single cell Flux Estimation Analysis), to infer single cell fluxome from single cell RNA-sequencing (scRNA-seq) data. scFEA is empowered by a comprehensively reconstructed human metabolic map into a factor graph, a novel probabilistic model to leverage the flux balance constraints on scRNA-seq data, and a novel graph neural network based optimization solver. The intricate information cascade from transcriptome to metabolome was captured using multi-layer neural networks to fully capitulate the non-linear dependency between enzymatic gene expressions and reaction rates. We experimentally validated scFEA by generating an scRNA-seq dataset with matched metabolomics data on cells of perturbed oxygen and genetic conditions. Application of scFEA on this dataset demonstrated the consistency between predicted flux and metabolic imbalance with the observed variation of metabolite abundance in the matched metabolomics data. We also applied scFEA on five publicly available scRNA-seq and spatial transcriptomics datasets and identified context and cell group specific metabolic variations. The cell-wise fluxome predicted by scFEA empowers a series of downstream analysis including identification of metabolic modules or cell groups that share common metabolic variations, sensitivity evaluation of enzymes with regards to their impact on the whole metabolic flux, and inference of cell-tissue and cell-cell metabolic communications.