cssi/SciSciGPT-SciSciNet huggingface dataset:
Predictors of survival in coexistent hypersensitivity pneumonitis with autoimmune features

Abstract Background Hypersensitivity pneumonitis (HP), an immune-mediated inflammatory interstitial lung disease (ILD), can result from exposure to several well-recognized antigens. Despite antigen avoidance, progressive pulmonary fibrosis and death can occur, suggesting that additional factors may contribute to disease activity. We hypothesized that the presence of autoimmunity might impact clinical course in patients with HP. In this study, we examined an HP cohort to identify those with HP and autoimmune features (HPAF), and determine its prevalence and outcomes. Methods The University of Chicago ILD registry was screened to identify patients with HP. Patients were characterized as HPAF if they had an autoimmune disease or features of autoimmunity, defined as the presence of specific connective tissue disease (CTD) symptoms and serologies. Demographics, clinical characteristics, and outcomes were compared between groups. Survival analysis was performed using Cox regression to identify predictors of transplant-free survival in this cohort. Results One hundred twenty patients with chronic, fibrotic HP were identified. Of these, 18/120 (15%) were characterized as HPAF. Compared to those without evidence of autoimmunity, patients with HPAF had a higher proportion of females (54% vs. 83%, respectively; p = 0.02) but were otherwise similar with regard to clinical characteristics. The presence of autoimmunity was an independent predictor of increased mortality (HR 4.45; 95% CI 1.43–13.88; p = 0.01) after multivariable adjustment. Conclusions Fifteen percent of patients with chronic, fibrotic HP displayed evidence of a concurrent defined autoimmune disease or autoimmune features suggestive of CTD. The presence of autoimmunity in patients with chronic, fibrotic HP may portend a poorer prognosis. Future studies are needed to validate these findings and determine the impact of immunosuppressive treatment.
Cortisone-induced transformation of ovaries into testes in larval frogs.

SummaryCortisone, like 3 other tested alkyl substituted androstanes, causes the transformation of ovaries of frog larvae into testes. Its action is initially anti-ovariogenic, and sex reversal follows by a compensatory development of the meduallary rudiment. The dosages that produce sex reversal are high in comparison with the threshold values of testosterone and methyltestosterone.
Z-scans with excited-state reverse saturable absorption

The Z-scan of a particular porphine compound shows reverse saturable absorption in the focal region and saturable absorption in the wings. This reverse saturation occurs in the transition between the first and second excited states.
Evaluating the Improvement in Shear Wave Speed Image Quality Using Multidimensional Directional Filters in the Presence of Reflection Artifacts

Shear waves propagating through interfaces where there is a change in stiffness cause reflected waves that can lead to artifacts in shear wave speed (SWS) reconstructions. Two-dimensional (2-D) directional filters are commonly used to reduce in-plane reflected waves; however, SWS artifacts arise from both in- and out-of-imaging-plane reflected waves. Herein, we introduce 3-D shear wave reconstruction methods as an extension of the previous 2-D estimation methods and quantify the reduction in image artifacts through the use of volumetric SWS monitoring and 4-D-directional filters. A Gaussian acoustic radiation force impulse excitation was simulated in phantoms with Young’s modulus ( $E$ ) of 3 kPa and a 5-mm spherical lesion with $E = 6$ , 12, or 18.75 kPa. The 2-D-, 3-D-, and 4-D-directional filters were applied to the displacement profiles to reduce in-and out-of-plane reflected wave artifacts. Contrast-to-noise ratio and SWS bias within the lesion were calculated for each reconstructed SWS image to evaluate the image quality. For 2-D SWS image reconstructions, the 3-D-directional filters showed greater improvements in image quality than the 2-D filters, and the 4-D-directional filters showed marginal improvement over the 3-D filters. Although 4-D-directional filters can further reduce the impact of large magnitude out-of-plane reflection artifacts in SWS images, computational overhead and transducer costs to acquire 3-D data may outweigh the modest improvements in image quality. The 4-D-directional filters have the largest impact in reducing reflection artifacts in 3-D SWS volumes.
Connectome Networks: From Cells to Systems

Nervous systems are networks of neurons and brain regions that are structurally interconnected and dynamically linked in complex patterns. As mapping and recording techniques become increasingly capable of capturing neural structure and activity across widely distributed circuits and systems, there is a growing need for new analysis tools and modeling approaches to make sense of these rich “big data” sets. Modern network science offers a way forward. Both structural and functional brain data sets can be rendered in the form of complex networks and thus become amenable for network modeling and analysis, which can be carried out across scales, from the micro-scale of individual neurons to the macro-scale of whole-brain recordings. In this article, I sketch an overview of structural and functional brain network studies ranging from cells to systems. My emphasis will be on common themes in mapping network attributes across scales. In addition to highlighting important advances, I will outline some major challenges that need to be overcome to achieve a more complete understanding of connectome networks.
A Research on Safety Evaluation of Reconstruction Project in Design Phase

A new quantitative safety approach integrating the three evaluation methods was presented in the paper,road dangerous index(RDI) method.RDI that comprehensively quantitatively measured the relative safety performance of a road was formulated with linear weighting model by combining four risk indexes: highway design potential hazard index and safety guarantee of traffic facilities index established from road safety audit checklists;traffic flow safety index extracting safety inspection results of operating speed consistency;and accident index transformed from the results of accident analysis.The procedure was used to evaluate Dayun reconstruction project of Shanxi province in design phase,the road was divided into 13 road segments,RDI value of each road segment was calculated,as a result,it was conveniently and quickly to identify relative safety conditions between road segments,and to take effective measures to improve the design of the road dangerous segments.
Functional Plasticity of Adipose-Derived Stromal Cells During Development of Obesity

UNLABELLED Obesity is a major risk factor for a number of chronic diseases, including diabetes, cardiovascular diseases, and cancer. Expansion of the adipose mass requires adipocyte precursor cells that originate from multipotent adipose-derived stromal cells (ASCs), which in turn also participate in repair activities. ASC function might decline in a disease milieu, but it remains unclear whether ASC function varies during the development of obesity. We tested the hypothesis that microenvironmental inflammatory changes during development of metabolic disorders in obesity affect ASC function. Domestic pigs were fed with an atherogenic (n = 7) or normal (n = 7) diet for 16 weeks. Abdominal adipose tissue biopsies were collected after 8, 12, and 16 weeks of diet for ASC isolation and immunohistochemistry of in situ ASCs and tumor necrosis factor-α (TNF-α). Longitudinal changes in proliferation, differentiation, and anti-inflammatory functions of ASCs were assessed. At 16 weeks, upregulated TNF-α expression in adipose tissue from obese pigs was accompanied by increased numbers of adipocyte progenitors (CD24(+)/CD34(+)) in adipose tissue and enlarged adipocyte size. In vitro, ASCs from obese pigs showed enhanced adipogenic and osteogenic propensity, which was abolished by anti-TNF-α treatment, whereas lean ASCs treated with TNF-α showed enhanced adipogenesis. Furthermore, obese ASCs showed increased senescence compared with lean ASCs, whereas their immunomodulatory capacity was preserved. Adipose tissue inflammation promotes an increase in resident adipocyte progenitors and upregulated TNF-α enhances ASC adipogenesis. Thus, adipose tissue anti-inflammatory strategies might be a novel target to attenuate obesity and its complications. SIGNIFICANCE Adipose-derived stromal cell (ASC) function might decline in a disease milieu, but it remains unclear whether ASC function varies during the development of obesity. This study tested the hypothesis that microenvironmental inflammatory changes during development of metabolic disorders in obesity affect ASC function. It was found that ASCs show increased propensity for differentiation into adipocytes, which is partly mediated by upregulated tumor necrosis factor-α (TNF-α), likely in their adipose tissue microenvironment. Furthermore, TNF-α magnified obese ASC senescence, although it did not regulate their anti-inflammatory properties. Thus, adipose tissue inflammation might be a novel therapeutic target to avert ASC maldifferentiation and senescence.
Poor biofilm forming ability and long-term survival of invasive Salmonella Typhimurium ST313

Salmonella enterica serovar Typhimurium, an enteric pathogen that causes a self-limiting gastroenteritis, forms biofilms on different surfaces. In sub-Saharan Africa, Salmonella Typhimurium of a novel sequence type (ST) 313 was identified and produces septicemia in the absence of gastroenteritis. No animal reservoir has been identified, and it is hypothesized that transmission occurs via human to human. In this study, we show that invasive Salmonella Typhimurium ST313 strains from Mali are poor biofilm producers compared to Salmonella Typhimurium ST19 strains, which are found worldwide and are known to be associated with gastroenteritis. We evaluated biofilms using crystal violet staining, examination of the red, dry and rough morphotype, pellicle formation and a continuous flow system. One month-old Salmonella Typhimurium ST19 colonies survived in the absence of exogenous nutrients and were highly resistant to sodium hypochlorite treatment compared to Salmonella Typhimurium ST313. This study for the first time demonstrates the comparative biofilm-forming ability and long-term survival of clinical Salmonella Typhimurium ST19 and ST313 isolates. Salmonella Typhimurium ST19 strains are strong biofilm producers and can survive desiccation compared to Salmonella Typhimurium ST313 that form weak biofilms and survive poorly following desiccation. Our data suggest that like Salmonella Typhi, Salmonella Typhimurium ST313 lack mechanisms that allow it to persist in the environment.
Quantification of neural functional connectivity during an active avoidance task

Many behavioral and cognitive processes are associated with spatiotemporal dynamic communication between brain areas. Thus, the quantification of functional connectivity with high temporal resolution is highly desirable for capturing in vivo brain function. However, brain functional network quantification from EEG recordings has been commonly used in a qualitative manner. In this paper, we consider pairwise dependence measures as random variables and estimate the pdf for each electrode of the arrangement. A metric imposed by the quadratic Cauchy-Schwartz Mutual Information quantifies these pdfs. We present the results by brain regions simplifying the analysis and visualization drastically. The proposed metric of functional connectivity quantification is addressed for temporal dependencies of the brain network that can be related to the task.
Molecular and Cellular Specialization of Iron Regulation In Human Erythroid Progenitor Cells Prior to Hemoglobin Production

Abstract 4255 Based upon the importance of iron for erythropoiesis, it was hypothesized that specific molecular and cellular mechanisms may be manifested during early erythropoiesis in preparation for heme and hemoglobin production. Here iron regulation was studied in immature erythroid progenitor cells prior to the increased production of heme or hemoglobin. CD34+ cells were cultured in SCF, IL-3 and FLT-3 ligand for 7 days, and the erythroid progenitor cells were identified and sorted from three donors according to the differential expression of CD36, CD41, and CD71. Among the sorted populations, the CD71(+)CD36(+)CD41(-)GPA(-) cells grew almost exclusively (>95%) into erythroid colonies in methylcellulose culture. Cytospin examination of those erythroid progenitor cells demonstrated large blasts with deep blue cytoplasm and blebbed membranes consistent with pre-proerythroblasts. Furthermore, heme accumulation and hemoglobin were absent. Western analyses revealed that ferritin, transferrin receptor 1 (TfR1), and transferrin receptor 2 (TfR2) expression were regulated by dosed titrations (0, 10, 20, 40, 60, and 100 %) of iron-saturated transferrin in the culture medium. The intracellular iron-storage protein, ferritin, showed increased expression with higher holo-transferrin saturation. Opposite patterns of iron-dependent regulation for the transferrin receptors was identified. TfR1 protein decreased and TfR2 increased with increased transferrin saturation. While TfR1 was detected at high levels on the plasma membranes, immunofluorescence studies showed TfR2 co-localization with lysosomes (correlation with LAMP1, a lysosomal marker, R = 0.53 ± 0.11, n=22). Decreased holo-transferrin in the culture medium resulted in no significant reduction in the proliferation of these cells until hemoglobin production was induced by erythropoietin. Confocal microscopy demonstrated a distinct peri-centrosomal lysosomal compartment surrounded by mitochondria. Coincidentally, upon sulfide-silver staining, it was observed that iron accumulated within the lysosomal compartment in a transferrin-dependent fashion. No similar iron-containing lysosomal-mitochondrial structure was identified in non-erythroid cells in the same cultures. These results suggest that functional, lineage-specific differentiation occurs at the progenitor stage of hematopoiesis, and that iron import and regulation is highly developed during erythropoiesis prior to hemoglobin production. Disclosures: No relevant conflicts of interest to declare.
Naturalizing Africa: Ecological Violence, Agency, and Postcolonial Resistance in African Literature

The problem of environmental degradation on the African continent is a severe one. In this book, Cajetan Iheka analyzes how African literary texts have engaged with pressing ecological problems in Africa, including the Niger Delta oil pollution in Nigeria, ecologies of war in Somalia, and animal abuses. Analyzing narratives by important African writers such as Amos Tutuola, Wangari Maathai, J. M. Coetzee, Bessie Head, and Ben Okri, Iheka challenges the tendency to focus primarily on humans in the conceptualization of environmental problems, and instead focuses on how African literature demonstrates the interconnection and 'proximity' of human and nonhuman beings. Through this, Iheka ultimately proposes a revision of the idea of agency based on human intentionality in African literary studies and postcolonialism: that texts yoke the exploitation of Africans to the despoliation of the environment, and they recommend responsibility toward human and nonhuman beings as crucial for ecological sustainability and addressing climate change.
The Influence of Green Density upon Sintering

The primary characteristic of a ceramic compact prior to sintering is its green density. The green density obviously determines the amount of shrinkage required to densify a ceramic, but its influence upon the densification rate or the microstructure of the ceramic is not well understood. A full description of microstructure development must include the role of green density. Green density effects are also important in understanding processing-related defects. Green density inhomogeneities on a microscopic scale have recently figured in models of the development of strength-limiting flaws in ceramics [1,2].
Genetic and cellular control of spontaneous autoimmune thyroiditis in OS chickens.

Starting in 1956 (1) R. K. Cole selected a substrain of phenotypically hypothyroid chickens from the White Leghorn Cornell C strain (CS), eventually establishing the Obese strain (OS). OS and CS flocks are maintained at Cornell University, Ithaca, New York, by closed matings that purposely avoid inbreeding (2). Three additional sublines of OS, viz., OSA, OSB, and OSC, are produced by sib matings in the authors1 laboratory for the purpose of developing inbred OS lines (3).
USE OF THE VELOCITY OF ULTRASOUND TO DETERMINE THE PHASE VOLUME OF DISPERSIONS

A technique to determine concentration profiles in non-aerated dispersions from the velocity of ultrasound V is described. A pulse-overlap method is used to obtain the values of V at each height over the dispersion. A concentration profile is easily obtained from the velocity values, and its variation with time allows the detailed study of sedimentation/creaming processes. We present concentration profiles for an electrostaticallystabilised latex dispersion and for alkane-in-water emulsions in the presence and absence of non-adsorbing polymer (which induces flocculation). The data are compared with the theoretical profiles for a dispersion of non-interacting, monodisperse hard spheres. Changes in concentration profile are detected before they are visually apparent and the technique has industrial applications in product development and quality control.
Delayed Sleep-Phase Type

Delayed sleep-phase disorder (DSPD) is a disorder in which the major sleep episode is delayed in relation to the desired clock time, which results in symptoms of sleep-onset insomnia or difficulty in awakening at the desired time. DSPD patients typically report an inability to fall asleep before about 2.00 a.m., and may experience difficulty with sleep onset until as late as 6.00 a.m. Although likely the most prevalent circadian-rhythm sleep disorder, DSPD is nonetheless relatively rare, affecting ∼1% of the population, and 7–10% of patients with disorders of initiating or maintaining sleep. While there is evidence for the biological basis of ‘adolescent’ delayed sleep phase, it is not clear whether this is an equivalent phenomenon to DSPD, which has been linked to certain genetic mutations. DSPD has been successfully treated with chronotherapy, timed bright light exposure, and exogenous melatonin, but all current treatments require substantial compliance, and for many patients, lifelong maintenance of treatment.
Embodiment, Anthropomorphism, and Intellectual Property Rights for AI Creations

Computational creativity is an emerging branch of artificial intelligence (AI) concerned with algorithms that can create novel and high-quality ideas or artifacts, either autonomously or semi-autonomously in collaboration with people. Quite simply, such algorithms may be described as artificial innovation engines. These technologies raise questions of authorship/inventorship and of agency, which become further muddled by the social context induced by AI that may be physically-embodied or anthropomorphized. These questions are fundamentally intertwined with the provision of appropriate incentives for conducting and commercializing computational creativity research through intellectual property regimes. This paper reviews current understanding of intellectual property rights for AI, and explores possible framings for intellectual property policy in social context.
The Political Alignment of Business in Africa

Under what conditions will business elites in Africa shift their electoral support from incumbent leaders to opposition challengers? I argue in this paper that business remains allied to the political status quo where incumbents manage to sustain the state’s traditional role as gatekeeper to financial markets through capital, credit, and currency controls. But in countries obliged to undertake liberalizing reforms, business becomes free to diversify its campaign contributions, if not offer outright support to the opposition, as incumbents lose their capacity to punish defections through financial reprisals. To provide evidence for this argument, I use data on presidential tenure in the chambers of commerce for 30 African countries to show how the business-state relationship is shaped by financial controls. I then contrast the cases of Kenya and Cameroon to demonstrate how the removal of such controls can determine the timing and the orientation of business’ political alignment.
Impact of the Affordable Care Act on early-stage diagnosis and treatment for women with ovarian cancer.

LBA5563Background: The 2010 Affordable Care Act (ACA) expanded access to insurance and care for many Americans. Our objective was to evaluate the impact of the ACA on stage at diagnosis and time to...
Control of Network Opinion Dynamics by a Selfish Agent with Limited Visibility

Abstract Manipulation of a linear network opinion dynamics by a single selfish agent is considered. The selfish agent is modeled as measuring a projection (statistic) of current network opinions, which may be either myopic or global. The agent then enacts a local feedback control using this measurement. The selfish agent’s ability to manipulate network-wide opinions to a desired reference is assessed, both under nominal conditions and in the presence of a second, stubborn agent. Specifically, it is shown that low-gain proportional and proportional-integral controllers can be applied to manipulate network-wide opinions or opinion statistics. A nonlinear variant on the opinion-dynamics model, where the agents’ opinions are capped, is also briefly studied. The control strategies are illustrated using a 62-node dolphin social network model.
Make Your Own Deep Inferior Epigastric Artery Perforator Flap: Perforator Delay Improves Deep Inferior Epigastric Artery Perforator Flap Reliability

Abdominal-based autologous breast reconstruction remains a conflict between blood supply and donor site complication. Optimizing esthetics and minimizing recovery and postoperative pain add further complexity. We present a 2-stage technique of deep inferior epigastric artery perforator flap reconstruction to (1) reliably harvest single-vessel flaps while minimizing fat necrosis, (2) decrease abdominal wall morbidity, and (3) improve breast and donor site esthetics. Methods Female subjects presenting between August 2017 and January 2019 to the senior surgeon for abdominal-based breast reconstruction were included. After mastectomy, the subjects underwent subcutaneous placement of tissue expanders and in situ selection of a low, centrally located perforator based on preoperative computed tomographic angiography imaging through an infraumbilical "T" incision with ligation of all other perforators and superficial system. Subjects underwent tissue expander explant and flap transfer at a second stage. Results One hundred thirty-five subjects undergoing 215 free flaps met criteria. Mean age and body mass index were 52.1 years and 29.3 kg/m2, respectively. Seven perforator complications (3.3%) occurred with 2 (0.9%) total and 5 (2.3%) partial flap losses. There were 20 (14.8%) readmissions and 26 (19.3%) reoperations. Breast complications included arterial thrombosis (0.5%), venous congestion (1.9%), and fat necrosis (5.1%). The mastectomy skin flap necrosis rate decreased from 14.9% to 2.3% following staged reconstruction. Abdominal donor site complications included delayed healing (11.1%), seroma (5.9%), and hematoma (2.2%). Conclusions The 2-stage delayed deep inferior epigastric artery perforator flap technique represents a safe, efficacious modality to allow for reliable harvest of single-vessel flaps with low rates of fat necrosis while improving donor site esthetics and morbidity.
Assessment of loss‐of‐control eating in healthy youth by interview and questionnaire

OBJECTIVE The aim of this study is to evaluate two questionnaires, an updated youth version of the questionnaire on eating and weight patterns (Questionnaire on Eating and Weight Patterns-5 Children/Adolescent [QEWP-C-5]) and the Loss-of-Control (LOC) Eating Disorder Questionnaire (LOC-ED-Q), against the Eating Disorder Examination (EDE) interview to assess the presence of LOC-eating among youth. METHOD Two-hundred and eighteen youths (12.8 ± 2.7 years) completed the QEWP-C-5, LOC-ED-Q, and EDE, depressive and anxiety questionnaires, and adiposity assessment. Sensitivity, specificity, positive-predictive value, negative-predictive value, and diagnostic accuracy were calculated; Cochran's Q and McNemar's tests were used to compare measures. Receiver operating characteristic area under the curve (AUC) analyses were performed. Mood and adiposity based on LOC-eating presence and absence based on each measure were examined. RESULTS The QEWP-C-5 and LOC-ED-Q demonstrated poor sensitivity (33%; 30%) and high specificity (95%; 96%) compared with the EDE. The AUCs suggested neither the QEWP-C-5 (0.64) nor the LOC-ED-Q (0.62) demonstrated acceptable diagnostic accuracy. Comparing distributions of LOC-eating presence between assessments, the QEWP-C-5 and EDE did not differ significantly (p = .10), while the LOC-ED-Q and EDE had significantly different distributions (p = .03). LOC-eating presence was associated with higher depressive and anxiety symptoms across all measures (ps < .02). Greater adiposity (ps < .02) was associated with LOC-eating presence on the EDE and LOC-ED-Q, and higher BMI z-score (p = .02) on the LOC-ED-Q. DISCUSSION Neither the QEWP-C-5 nor the LOC-ED-Q was sensitive for identifying LOC-eating presence as determined by the EDE, although both were associated with greater mood symptoms. Research is needed to improve self-report questionnaires to better screen for LOC-eating presence among pediatric populations.
Chapter 11 – Gap Junctions

Electrotonic coupling between cells is accomplished through the formation of gap junctions (GJs) between cells. Composed of connexin proteins, GJs are found on multiple cell types and connexin distribution is cell type-specific. All GJs play a role in cellular communication, but astrocytic GJs are thought to play a role in K+ and glutamate redistribution, synaptic strength regulation, and memory formation. Both human tissue studies and animal models of epilepsy have shown considerable changes in connexin expression after seizure activity. Electrophysiological studies have implicated GJs in the generation of very fast oscillations that precede seizures. Knockout and GJ inhibitors studies have demonstrated potential anticonvulsant effects, although these results are mixed and suffer from lack of specificity of many of the currently available GJ inhibitors. Findings implicating GJs in epilepsy as well as differences in the roles of neuronal versus glial GJs in tissue excitability are considered in this chapter.
Smart Agriculture Based on IoT and Cloud Computing

The improvement in new technologies in this modern era has resulted to miniaturization of sensors and the attempts to utilize them in various areas are getting succeeded. Also, adoption of Internet of Things (IoT) and Cloud Computing in any area are leading them to a notion of "Smart" like Smart Health Care systems, Smart Cities, Smart Mobility, Smart Grid, Smart Home and Smart Metering etc. One such area of research that has also seen this adoption is agriculture and thus making it a Smart Agriculture. Agriculture is one of the major source for any of the largest population countries like India, China etc. to earn money and carry out the livelihood. Involvement of IoT and Cloud Computing in the agricultural sector would result in the better production of crops by controlling the cost, monitoring performance and maintenance, thereby benefiting the farmers and the overall nation. This paper focuses on introduction of a Smart Drone for crop management where the real-time Drone data coupled with IoT and Cloud Computing technologies help in building a sustainable Smart Agriculture.
Neutrophil-lymphocyte score: A novel prognostic scoring system that utilized the dynamic change of neutrophil, lymphocyte, and albumin and its comparison to other indices.

3048Background: Indications for immune checkpoint inhibitor (ICI) in cancer care are expanding rapidly. There is increasing need for accurate decision tool to better guide treatment. We have constr...
Automated prediction and annotation of small proteins in microbial genomes

Abstract Recent work performed by Sberro et al. (2019) revealed a vast unexplored space of small proteins existing within the human microbiome. At present, these small open reading frames (smORFs) are unannotated in existing reference genomes and standard genome annotation tools are not able to accurately predict them. In this study, we introduce an annotation tool named SmORFinder that predicts small proteins based on those identified by Sberro et al. This tool combines profile Hidden Markov models (pHMMs) of each small protein family and deep learning models that may better generalize to smORF families not seen in the training set. We find that combining predictions of both pHMM and deep learning models leads to more precise smORF predictions and that these predicted smORFs are enriched for Ribo-Seq or MetaRibo-Seq translation signals. Feature importance analysis reveals that the deep learning models learned to identify Shine-Dalgarno sequences, deprioritize the wobble position in each codon, and group codons in a way that strongly corresponds to the codon synonyms found in the codon table. We perform a core genome analysis of 26 bacterial species and identify many core smORFs of unknown function. We pre-compute small protein annotations for thousands of RefSeq isolate genomes and HMP metagenomes, and we make these data available through a web portal along with other useful tools for small protein annotation and analysis. The systematic identification and annotation of those important small proteins will help researchers to expand our understanding of this exciting field of biology.
Postoperative complication rates and hazards-model survival analysis of revision surgery following occipitocervical and atlanto-axial fusion

Abstract Background Complication rates following occipitocervical and atlanto-axial fusion are high. While methods to fuse the upper cervical spine levels have evolved, complication rates and surgical survivorship of occipitocervical fusion versus atlanto-axial fusion are incompletely understood. Methods The PearlDiver Research Program ( www.pearldiverinc.com ) was used to identify patients undergoing primary occipitocervical or atlanto-axial fusion between 2007 and 2017. Incidence of each fusion procedure was studied across time. Multivariable logistic regression was used to compare 30-day readmission, 30-day medical complications, and post-operative opioid utilization at 1, 3, 6, and 12 months between cohorts, controlling for age, gender, Charlson Comorbidity Index (CCI), and indication for surgery. Risk of revision was compared through Cox-proportional hazards modeling, Kaplan-Meier survival, and log-rank test. Results Cohorts of 483 occipitocervical fusions and 737 atlanto-axial fusions were examined. From 2008 to 2016, incidence of occipitocervical fusion rose 55.9%, whereas atlanto-axial fusion rose 21.6%. A greater percentage of atlanto-axial fusions were due to trauma (69.9% vs. 50.5%), whereas a greater percentage of occipitocervical fusions were due to degenerative disease (41.6% vs. 29.4%) (p = 0.0161). Total 30-day complications were seen in 40.9% of occipitocervical fusion patients compared to 26.3% of atlanto-axial fusion patients (aOR=2.06, p Conclusions Rates of occipitocervical and atlanto-axial fusion are rising, while complication and revision surgery rates remain high, with occipiticervical fusion leading to higher rates even after controlling for patient characteristics and surgical indication. Spine surgeons should be cautious when considering fusion of the occipitocervical levels if atlanto-axial fusion could be performed safely and provide adequate stabilization to treat the same pathology.
Magneto-optical investigation of scattering by superparamagnetic nanoparticles using multi-harmonic analysis

Magnetic nanoparticles (MNPs) are widely used in imaging, magnetic hyperthermia, drug delivery, etc. We present a continuation of our study of dilute aqueous suspensions of magnetite nanoparticles using an AC Faraday rotation setup. Our previous results focused on analyzing the first and higher odd harmonics of the magnetic field frequency yielding the average particle magnetic moment μ, particle density n, and Verdet constant of the sample. Here, we investigate the leading even harmonic (2f) signal to analyze scattering by constructing a scattering ratio. This signal is independent of the polarization state of the incident light and is therefore not relatable to Faraday rotation (FR). The evidence of MNP clustering along with the geometric shadowing effect may explain the scattering response as a function of magnetic field frequency and amplitude. Investigation of clusters in SNPs is critical to establish their effective moment and size as a function of magnetic field profile. This analysis can provide a consistency check on the odd harmonic analysis, in addition to providing a physical picture of the underlying process of cluster formation. We have measured the scattering response of magnetite (Fe3O4) nanoparticles that vary in size from 15 to 25 nm along with two different types of SNPs with the same core diameter (20 nm) but different functionalization layers (Oleic acid and PEG). To explain the change in light intensity as a function of magnetic field, we are developing a model that employs a field-dependent cross-section which we hope to relate to cluster size.
Clawback Provision of SOX, Financial Misstatements, and CEO Compensation Contracts

Section 304 of the Sarbanes-Oxley Act (hereafter, SOX), commonly known as the clawback provision, entitles the SEC to sue the CEO and CFO in an attempt to recover their incentive compensation based on misstated financial reports. While a stream of literature investigates the effects of voluntary firm-initiated clawback provisions, this study explores the effects of the mandatory SOX clawback provision on the likelihood of financial misstatements and CEO compensation. We find a significant decrease in the association between CEO in-the-money option value and the likelihood of a misstatement from the pre- to the post-SOX period, suggesting the SOX clawback provision has been effective in reducing financial misstatements arising from CEO in-the-money stock options. To examine the effects of the SOX clawback provision on CEO compensation, we identify a set of misstatement firms with high restatement likelihood where the CEOs are most likely concerned with the impact of the SOX clawback provision on their compensation. We then compare how the compensation of CEOs in these high restatement likelihood firms changes between the pre- and post-SOX periods with the compensation of CEOs in control firms. We find that compared to the control firms, these firms with a high restatement likelihood where the CEO is the chair of the board exhibit an increase in CEO salaries between the pre- and the post-SOX periods, suggesting that in the post-SOX period influential CEOs are able to receive higher salaries which are not subject to the SOX clawback provision.
The use of abaloparatide to treat nonunion following dorsal closing wedge osteotomy for Freiberg's disease: A case report.

A middle-aged woman who was previously a long-distance trail runner presented with chronic right forefoot pain and was diagnosed with Freiberg's disease. She suffered from nonunion after undergoing a dorsal closing wedge osteotomy. The nonunion achieved full osseous union after treatment with abaloparatide. Patient reported outcome measures taken at 19 months postoperatively indicated good to excellent clinical outcomes and satisfaction. The aim of this case is to report on the effectiveness of abaloparatide to treat nonunion and support fracture healing.
Enhanced recovery after surgery protocol and postoperative opioid prescribing for cesarean delivery: an interrupted time series analysis

Enhanced recovery after surgery (ERAS) pathways have emerged as a promising strategy to reduce postoperative opioid use and decrease the risk of developing new persistent opioid use in surgical patients. However, the association between ERAS implementation and discharge opioid prescribing practices is unclear. We conducted a retrospective observational quasi-experimental study of opioid-naive patients aged 18+ undergoing cesarean delivery between February 2015 and December 2019 at a large academic center. An interrupted time series analysis (ITSA) was used to model the changes in pain medication prescribing associated with the implementation of ERAS to account for pre-existing temporal trends. Among the 1473 patients (out of 2249 total) who underwent cesarean delivery after ERAS implementation, 80.72% received a discharge opioid prescription vs. 95.36% at baseline. Pre-ERAS daily oral morphine equivalents (OME) on the discharge prescription decreased by 0.48 OME each month (p<0.01). There was a level shift of 35 more OME prescribed (p<0.01), followed by a monthly decrease of 1.4 OMEs per month after ERAS implementation (p<0.01). Among those who received a prescription, 61.35% received a total daily dose greater than 90 OME compared to 11.35% pre-implementation (p<0.01), while prescriptions with a total daily dose less than 50 OME decreased from 79.86 to 25.85% after ERAS implementation(p<0.01). Although ERAS implementation reduced the overall proportion of patients receiving a discharge opioid prescription after cesarean delivery, for the subset of patients receiving an opioid prescription, ERAS implementation may have inadvertently increased the prescribing of daily doses greater than 90 OME. This finding highlights the importance of early and continued evaluation after new policies are implemented.
The Research Imagination: An Introduction to Qualitative and Quantitative Methods

The idea that science is a blueprint for research, and imagination gives research its life and purpose inspired this comprehensive explanation of research methodology. The authors' decades of experience have revealed that research is a craft requiring judgment and creativity, not simply memorization and application of the rules of science. Whether one is conducting an intimate one-on-one interview or a large-scale examination of an entire society, human imagination and scientific principles of inquiry go hand in hand. To that end, this book emphasizes scientific method, but also acknowledges its critics. It covers a wide variety of data-collection techniques, but presents them as reinforcing rather than competing with one another, thus striking a balance between qualitative and quantitative methods. It is designed for students and instructors who want a comprehensive treatment of a variety of research techniques with special emphasis on qualitative approaches.
Septra® (Burroughs Wellcome)

The combination of a folic acid antagonist and a sulfonamide inhibits two consecutive steps in the biosynthesis of nucleic acids and proteins essential to many bacteria. The two compounds are synergistic against many common urinary and other type infections.
Policing paternity: historicising masculinity and sexuality in early-modern France

In early-modern working communities, masculinity for young lower-rank men was embedded in particular performances and practices of licit intimacy. This essay analyses the specific expectations and parameters for men as well as women through which communities acknowledged and validated expressions of youth sexuality while marking and policing boundaries beyond which youthful courtship could become threatening to household and neighbourhood stability. Young men and women were the focus of these efforts just as they themselves participated in the assessment of appropriate behaviour. These issues suggest an on-going negotiation and contestation about what was appropriate for single men and women in terms of intimacy, and a clear sense that a violation of the community norms carried consequences for men as well as women.
Central Bank Independence Revisited

The recent financial crisis has drawn attention to the interactions between monetary and fiscal policies and their potential implications for central bank independence. I focus on aspects of these interactions. First, is central bank independence meaningless with fiscal acquiescence? And does central bank independence threatens potential gains from monetary and fiscal policy coordination?
A retrospective study on the efficacy of pubic symphysis corticosteroid injections in the treatment of pubic symphysis pain.

Objective. To report immediate and follow-up pain intensity outcomes of fluoroscopically guided contrast- enhanced pubic symphysis corticosteroid injections for patients with pubic symphysis pain (PSP). Design. Retrospective medical record review. Setting. Outpatient rehabilitation clinic. Subjects. Patients with PSP who underwent pubic symphysis corticosteroid injection (PSI). Intervention. Pubic symphysis corticosteroid injection. Outcome Measures. Pain intensity as measured by numeric rating scale (NRS). Results. Fourteen patients (4 men and 10 women) underwent PSI. Five patients had PSP for less than 6 months, nine had chronic pain (>than 6 months). In 7 of the 10 women the pain was pregnancy related. All patients received other treatments prior to injection. Pubic symphysis tenderness was the most common physical examination finding (13/14 patients). Follow-up pain intensity (PI)-NRS improvement of greater than 2 points was considered clinically significant. At follow-up, improvement was not statistically significant (Wilcoxon signed-rank test, z = 1.62 P = 0.10). Patients with pain 6 months (Fisher's exact test, P = 0.775). Conclusions. PSIs do not provide clinically or statistically significant relief at follow-up in patients with PSP.
Expression in Escherichia coli, purification and kinetic characterization of human heparan sulfate 3-O-sulfotransferase-1.

Heparan sulfate (HS) glycosaminoglycans are a structurally diverse class of complex biomolecules that modulate many important events at the cell surface and within the extracellular matrix and whose structural heterogeneity derives largely from the sequence-specific N- and O-sulfations catalyzed by an extensive repertoire of sulfating enzymes. We have expressed the human heparan sulfate 3-OST-1 isoform in Escherichia coli and subsequently purified a soluble, active enzyme. To assess its functionality, we determined the kinetic parameters for the recombinant 3-O-sulfotransferase-1 using a radiochemical assay that directly measures the 3-O-sulfation of unlabeled bovine kidney heparan sulfate in vitro using [35S]PAPS as the sulfate donor. The apparent Km values measured were in the low micromolar range (KHSm = 4.3 μM; KPAPSm = 38.6 μM); Vmax values of 18 and 21 pmol sulfate/min/pmol of enzyme for HS and PAPS, respectively. These values were compared with kinetic parameters likewise measured for recombinant 3-OST-1 purified from baculovirus-infected sf9 cells. The two enzymes appear to modify heparan sulfate in vitro to roughly the same extent and with comparable specificities. The expression of 3-OST-1 in E. coli represents an important step in subsequent structure–function studies.
Structure of the Amino Terminus of a Gap Junction Protein

Charged amino acid residues in the amino terminus of gap junction forming proteins (connexins) form part, if not all, of the transjunctional voltage sensor of gap junction channels and play a fundamental role in ion permeation. Results from studies of the voltage dependence of N-terminal mutants predict that residues 1-10 of Group I connexins lie within the channel pore and that the N-terminus forms the channel vestibule by the creation of a turn initiated by the conserved G12 residue. Here we report that intercellular channels containing mutations of G12 in Cx32 to residues that are likely to interfere with flexibility of this locus (G12S, G12Y, and G12V) do not express junctional currents, whereas a connexin containing a proline residue at G12 (Cx32G12P), which is expected to maintain a structure similar to that of the G12 locus, forms nearly wild-type channels. We have solved the structure of an N-terminal peptide of Cx26 (MDWGTLQSILGGVNK) using 1H 2D NMR. The peptide contains two structured domains connected by a flexible hinge (domain-hinge-domain motif) that would allow the placement of the amino terminus within the channel pore. Residues 1-10 adopt a helical conformation and line the channel entrance while residues 12-15 form an open turn. Overall, there is good agreement between the structural and dynamic features of the N-terminal peptide provided by NMR and the functional studies of the voltage dependence of channels formed by wild-type and N-terminal mutations.
Thermodynamic Analysis of the CSL·Notch Interaction: DISTRIBUTION OF BINDING ENERGY OF THE NOTCH RAM REGION TO THE CSL β-TREFOIL DOMAIN AND THE MODE OF COMPETITION WITH THE VIRAL TRANSACTIVATOR EBNA2

The Notch signaling pathway is a cell-cell communication network giving rise to cell differentiation during metazoan development. Activation of the pathway releases the intracellular portion of the Notch receptor to translocate to the nucleus, where it is able to interact with the effector transcription factor CSL, converting CSL from a transcriptional repressor to an activator. This conversion is dependent upon the high affinity binding of the RAM region of the Notch receptor to the β-trefoil domain (BTD) of CSL. Here we probe the energetics of binding to BTD of each conserved residue of RAM through the use of isothermal titration calorimetry and single residue substitution. We find that although the highly conserved ΦWΦP motif is the largest determinant of binding, energetically significant interactions are contributed by N-terminal residues, including a conserved Arg/Lys-rich region. Additionally, we present a thermodynamic analysis of the interaction between the Epstein-Barr virus protein EBNA2 with BTD and explore the extent to which the EBNA2- and RAM-binding sites on BTD are nonoverlapping, as proposed by Fuchs et al. (Fuchs, K. P., Bommer, G., Dumont, E., Christoph, B., Vidal, M., Kremmer, E., and Kempkes, B. (2001) Eur. J. Biochem. 268, 4639–4646). Combining these results with displacement isothermal titration calorimetry, we propose a mechanism by which the ΦWΦP motif of RAM and EBNA2 compete with one another for binding at the hydrophobic pocket of BTD using overlapping but specific interactions that are unique to each BTD ligand.
Evaluation of peer-graded assignments in a skills-based course sequence

Abstract Peer grading has been used in higher education to assist in the evaluation process and enhance student learning. One form of active learning relevant to pharmacy practice is written documentation using the subjective, objective, assessment, plan (SOAP) format. The purpose of this study was to evaluate the peer-grading process utilized for three SOAP note assignments for pharmacy students enrolled in a skills-based course sequence entitled Professional Skills Development (PSD). Objective were to compare student and faculty scores for assignments and gather the students' perceptions about the peer grading sessions. To each SOAP note was graded by a blinded peer in a class session and graded independently by the faculty instructor. A survey was given to the students after the third SOAP note session to assess their perceptions of the grading sessions. Results For each of the sessions, the peer SOAP note score was lower than the faculty score ( p n = 98) completed the survey. The majority strongly agreed or agreed that the instructions were clear, the checklists were easy to follow, their learning was enhanced, faculty guidance allowed them to effectively grade a peer's SOAP note, and peer grading should be used more frequently in the curriculum. Conclusion Peer grading is useful in evaluating student SOAP note assignments and perceived by students as a valuable learning exercise.