Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors related to clinical quality improvement for small practices using an EHR.

OBJECTIVE To analyze the impact of three primary care practice transformation program models on performance: Meaningful Use (MU), Patient-Centered Medical Home (PCMH), and a pay-for-performance program (eHearts). DATA SOURCES/STUDY SETTING Data for seven quality measures (QM) were retrospectively collected from 192 small primary care practices between October 2009 and October 2012; practice demographics and program participation status were extracted from in-house data. STUDY DESIGN Bivariate analyses were conducted to measure the impact of individual programs, and a Generalized Estimating Equation model was built to test the impact of each program alongside the others. DATA COLLECTION/EXTRACTION METHODS Monthly data were extracted via a structured query data network and were compared to program participation status, adjusting for variables including practice size and patient volume. Seven QMs were analyzed related to smoking prevention, blood pressure control, BMI, diabetes, and antithrombotic therapy. PRINCIPAL FINDINGS In bivariate analysis, MU practices tended to perform better on process measures, PCMH practices on more complex process measures, and eHearts practices on measures for which they were incentivized; in multivariate analysis, PCMH recognition was associated with better performance on more QMs than any other program. CONCLUSIONS Results suggest each of the programs can positively impact performance. In our data, PCMH appears to have the most positive impact.
A Set Space Model for Feature Calculus

Processing natural language at the sentence level suffers from a sparse-feature problem caused by the limited number of words in a sentence. In this article, a Set Space Model (SSM) is proposed to utilize sentence information, the main idea being that, depending on structural characteristics or functional principles of linguistics, features in a sentence can be grouped into different sets. Feature calculus can then operate on the grouped features and capture structural information using external knowledge. The authors implement this method in a traditional information extraction task, with results showing significant and constant improvement in general information extraction.
Sortase A-mediated site-specific labeling of camelid single-domain antibody-fragments: a versatile strategy for multiple molecular imaging modalities.

A generic site-specific conjugation method that generates a homogeneous product is of utmost importance in tracer development for molecular imaging and therapy. We explored the protein-ligation capacity of the enzyme Sortase A to label camelid single-domain antibody-fragments, also known as nanobodies. The versatility of the approach was demonstrated by conjugating independently three different imaging probes: the chelating agents CHX-A"-DTPA and NOTA for single-photon emission computed tomography (SPECT) with indium-111 and positron emission tomography (PET) with gallium-68, respectively, and the fluorescent dye Cy5 for fluorescence reflectance imaging (FRI). After a straightforward purification process, homogeneous single-conjugated tracer populations were obtained in high yield (30-50%). The enzymatic conjugation did not affect the affinity of the tracers, nor the radiolabeling efficiency or spectral characteristics. In vivo, the tracers enabled the visualization of human epidermal growth factor receptor 2 (HER2) expressing BT474M1-tumors with high contrast and specificity as soon as 1 h post injection in all three imaging modalities. These data demonstrate Sortase A-mediated conjugation as a valuable strategy for the development of site-specifically labeled camelid single-domain antibody-fragments for use in multiple molecular imaging modalities. Copyright © 2016 John Wiley & Sons, Ltd.
Genome-wide screen uncovers novel pathways for tRNA processing and nuclear–cytoplasmic dynamics

In this resource, Wu et al. present the first comprehensive unbiased analysis of the role of nearly an entire proteome in tRNA biology and describe 162 novel and 12 previously known Saccharomyces cerevisiae gene products that function in tRNA processing, turnover, and subcellular movement. The findings from this genome-wide screen describe putative novel pathways for tRNA nuclear export and extensive links between tRNA biology and other aspects of cell physiology.
A phase II trial of dacomitinib, an oral pan-human EGF receptor (HER) inhibitor, as first-line treatment in recurrent and/or metastatic squamous-cell carcinoma of the head and neck.

BACKGROUND An open-label, multicenter, single-arm phase II trial was conducted to investigate the clinical activity of dacomitinib in recurrent/metastatic squamous-cell carcinoma of the head and neck (RM-SCCHN). PATIENTS AND METHODS Eligible patients were administered dacomitinib at 45 mg orally daily, in 21-day cycles. Primary end point was objective response rate. RESULTS Sixty-nine patients were enrolled with a median age of 62 years. Among response-evaluable patients, 8 [12.7%, 95% confidence interval (CI) 5.6% to 23.5%] achieved a partial response and 36 (57.1%) had stable disease, lasting ≥24 weeks in 9 patients (14.3%). The median progression-free survival (PFS) was 12.1 weeks and the median overall survival (OS) was 34.6 weeks. Most adverse events (AEs) were tolerable. The most common grade 3 or higher treatment-related AEs were diarrhea (15.9%), acneiform dermatitis (8.7%), and fatigue (8.7%). Treatment-related AEs led to at least one dose interruption in 28 (40.6%) patients and dose reductions in 26 (37.7%). Permanent treatment discontinuation occurred in 8 (11.6%) patients due to treatment-related AEs. CONCLUSIONS Dacomitinib demonstrated clinical activity in RM-SCCHN, and the primary end point of this study was met. The toxicity profile of this agent was generally manageable with dose interruptions and adjustments.
Awards

In 2001, the World Health Organization (WHO) ratified and published a new classification system, the International Classification of Functioning, Disability and Health (ICF). There has been a varying amount of discussion and debate across the health and disability fields about what the ICF means and what it has to offer. However, there has been little discussion of its use and value in the field of augmentative and alternative communication (AAC). This article describes the earlier International Classification of Impairments, Disabilities, and Handicaps (ICIDH), upon which the current ICF was based; and outlines the ICF and the preliminary, derived Child and Youth version of the ICF (ICF-CY). The article also proposes what the ICF has to offer the AAC field, from both a clinical and research perspective; and concludes with a discussion of the advantages and challenges of using the ICF.
Clinical course of patients with relapsed multiple myeloma.

OBJECTIVE To study the clinical course of patients with multiple myeloma (MM) that relapses after initial therapy. PATIENTS AND METHODS Patients with MM, seen at the Mayo Clinic in Rochester, Minn, between January 1, 1985, and December 31, 1998, were identified from a prospectively maintained database. Our study population consisted of 578 patients with newly diagnosed MM who were followed up and monitored throughout their clinical course at our institution. RESULTS The median age of the 578 patients with MM was 65 years (range, 26-92 years); 228 patients (39%) were women. The median follow-up of 71 surviving patients was 55 months (range, 0-202 months). The overall survival (OS) for the 578 patients at 1, 2, and 5 years was 72%, 55%, and 22%, respectively; the median OS from initial therapy was 28.4 months. The median OS of 355 patients who experienced relapse after initial treatment was 17.1 months from initiation of the second therapy, and 84% died within 5 years. The duration of response decreased consistently with each successive regimen. Patients with a high plasma cell labeling index (> or = 1.0%), low platelet count (< 150 x 10(9)/L), high creatinine level (> or = 2.0 mg/dL), and low albumin level (< 3.0 g/dL) had a poorer prognosis. CONCLUSIONS Our study revealed decreasing response duration with increasing number of salvage regimens, probably reflecting acquired drug resistance and an increasing proliferative rate of the myeloma cells. Patients who experienced relapse after initial treatment and received salvage therapy had a median survival of nearly 1.5 years. This must be remembered when making treatment decisions for these patients and must be factored in when assessing the efficacy of new therapies.
Approximate sum rate of distributed MIMO with ZF receives over semi-correlated K fading channels

The sum rate performance of distributed multiple-input multiple-output (D-MIMO) systems with Zero-Forcing (ZF) receivers over semi-correlated K fading channels involves special functions, which hinders us to further manipulations. To solve this issue, we derive the closed-form expressions of the achievable sum rate by using moment matching method, which is achieved by using a Gamma distribution to approximate the composite distribution. The derived expressions of the achievable sum rate incorporate multipath fading, shadow fading, and path loss. In order to get the insights into the effects of system and fading parameters on D-MIMO performance, the asymptotic behavior of the closed-form expression on the achievable sum rate at high signal-to-noise ratio (SNR) is explored. Finally, the massive MIMO systems analysis for large receiver antennas and transceiver antennas with fixed and finite ratio is pursued. The simulation results show that the proposed approach can accurately approximate analysis, especially for the large-scale systems.
Preventing depression in later life: translation from concept to experimental design and implementation.

OBJECTIVE The authors detail the public health need for depression prevention research and the decisions made in designing an experiment testing problem solving therapy as "indicated" preventive intervention for high-risk older adults with subsyndromal depression. Special attention is given to the recruitment of African Americans because of well-documented inequalities in mental health services and depression treatment outcomes between races. METHODS A total of 306 subjects (half white, half African American) with scores of 16 or higher on the Center for Epidemiological Studies of Depression Scale, but with no history of major depressive disorder in the past 12 months, are being recruited and randomly assigned to either problem solving therapy-primary care or to a dietary education control condition. Time to, and rate of, incident episodes of major depressive disorder are to be modeled using survival analysis. Level of depressive symptoms will be analyzed via a mixed models approach. RESULTS Twenty-two subjects have been recruited into the study, and to date eight have completed the randomly assigned intervention and postintervention assessment. Four of 22 have exited after developing major depressive episodes. None have complained about study procedures or demands. Implementation in a variety of community settings is going well. CONCLUSION The data collected to date support the feasibility of translating from epidemiology to RCT design and implementation of empirical depression prevention research in later life.
Effects of direct hemoperfusion with polymyxin B-immobilized fiber on rapidly progressive interstitial lung diseases.

OBJECTIVE Direct hemoperfusion with polymyxin B-immobilized fiber columns (PMX-DHP) has been used for the treatment of septic shock. It was recently suggested that PMX-DHP may also be effective in acute exacerbations of idiopathic pulmonary fibrosis (IPF). However, all previous reports are case series without controls. The aim of the study was to determine the effects of PMX-DHP on the prognosis of the patients with rapidly progressive interstitial lung diseases (ILDs) in a case-control setting. METHODS We herein retrospectively examined the clinical records of consecutive patients with acute exacerbation of IPF or rapidly progressive ILDs treated in our institute. We excluded those who had been treated with steroid pulse therapy for lung diseases, including those who had been taking more than 15 mg of oral prednisolone daily, or had undergone an operation within one month before the onset of acute respiratory failure. We compared the results of the laboratory tests and survivals between patients treated with and without PMX-DHP. RESULTS Twenty-six patients were enrolled in the study. Among them, 13 patients were treated with PMX-DHP in addition to immunosuppressive therapy, including steroid pulse therapy. The mean survival time of patients treated with PMX-DHP tended to be longer than patients not treated with PXM-DHP (p=0.067). Six patients who underwent PMX-DHP on the first day of steroid pulse therapy had significantly longer survival times than those who were treated with standard medication alone (p<0.01). CONCLUSION These results suggest that PMX-DHP performed on the first day of steroid pulse therapy may improve the prognosis of patients with rapidly progressive ILDs.
Expression of the mRNA of Seven Metabotropic Glutamate Receptors (mGluR1 to 7) in the Rat Retina. An In Situ Hybridization Study on Tissue Sections and Isolated Cells

We have studied the expression of mRNAs for seven metabotropic glutamate receptors (mGluR1–7) in the retina of the adult rat by in situ hybridization with tissue sections and isolated cells using [α35S]dATP‐labelled oligonucleotide probes. Hybridization revealed the expression of six of the metabotropic receptor mRNAs, mGluR1, 2 and 4–7, in the retina, while mGluR3 was not detected. Each of the expressed receptor mRNAs showed a distinct pattern of expression. In the outer nuclear layer, corresponding to photoreceptor somata, no labelling was detected. In the outer part of the inner nuclear layer, putative horizontal cells were labelled for mGluR5. More proximal in this layer, corresponding to the position of bipolar cell somata, there was strong labelling for mGluR6. A small number of bipolar cells were also labelled for mGluR5 and mGluR7. In situ hybridization with isolated cells showed that mGluR6 was expressed by rod bipolar cells. Subsets of amacrine cells, with cell bodies along the border between the inner nuclear layer and the inner plexiform layer, were positive for mGluR1, 2, 4 and 7, suggesting considerable heterogeneity of these receptors among amacrine cells. None of the seven metabotropic receptor mRNAs was expressed in isolated Müller glial cells. In the ganglion cell layer, virtually every ganglion cell and displaced amacrine cell was labelled for mGluR1 and mGluR4. Some cells in this layer (˜20% of the total), most likely both ganglion cells and displaced amacrine cells, were also labelled for mGluR2 and mGluR7. These findings suggest that metabotropic glutamate receptors are considerably more widespread among neurons in the retina than indicated by previous physiological and pharmacological investigations.
Mycobacterium indicus pranii induces dendritic cell activation, survival, and Th1/Th17 polarization potential in a TLR‐dependent manner

MIP is a nonpathogenic, soil‐borne predecessor of Mycobacterium avium. It has been reported previously that MIP possesses strong immunomodulatory properties and confers protection against experimental TB and tumor. DCs, by virtue of their unmatched antigen‐presentation potential, play a critical role in activation of antitumor and antimycobacterial immune response. The effect of MIP on the behavior of DCs and the underlying mechanisms, however, have not been investigated so far. In the present study, we showed that MIP induces significant secretion of IL‐6, IL‐12p40, IL‐10, and TNF‐α by DCs and up‐regulates the expression of costimulatory molecules CD40, CD80, and CD86. MIP(L) induced a significantly higher response compared with MIP(K). PI and Annexin V staining showed that MIP increases DC survival by inhibiting apoptosis. Consistently, higher expression of antiapoptotic proteins Bcl‐2 and Bcl‐xl was observed in MIP‐stimulated DCs. Cytokines, produced by nai¨ve T cells, cocultured with MIP‐stimulated DCs, showed that MIP promotes Th1/Th17 polarization potential in DCs. Response to MIP was lost in MyD88−/−DCs, underscoring the critical role of TLRs in MIP‐induced DC activation. Further studies revealed that TLR2 and TLR9 are involved in DC activation by MIP(L), whereas MIP(K) activates the DCs through TLR2. Our findings establish the DC activation by MIP, define the behavior of MIP‐stimulated DCs, and highlight the role of TLRs in MIP‐induced DC activation.
Total parathyroidectomy improves survival of hemodialysis patients with secondary hyperparathyroidism.

BACKGROUND AND AIMS To compare the prognosis of chronic hemodialysis patients with or without parathyroidectomy. METHODS Among 158 chronic hemodialysis patients who underwent total parathyroidectomy between July 1998 and April 2009, 88 patients were matched with 88 controls for sex, age, underlying disease and prior dialysis history. Then a retrospective evaluation of their prognosis was performed over a median observation period of 4.41 years. RESULTS The overall survival rate was 90.4% in the parathyroidectomy group and 67.4% in the control group. The cardiovascular death-free survival rate was 94.6% in the parathyroidectomy group and 76.3% in the control group. During observation, intact parathyroid hormone was measured every 6 months, and its average serum level was 37 ± 92 ng/L in the total parathyroidectomy group versus 274 ± 233 ng/L in the control group (p=0.0001). The total parathyroidectomy group had a significantly lower corrected calcium level and higher serum albumin level. Multivariate analysis revealed that parathyroidectomy, atrial fibrillation and serum albumin were significant factors for both total and cardiovascular mortality. CONCLUSION Total parathyroidectomy was associated with better survival, probably due to decreased cardiovascular mortality.
A multi-gene phylogeny of Lactifluus (Basidiomycota, Russulales) translated into a new infrageneric classification of the genus

Infrageneric relations of the genetically diverse milkcap genus Lactifluus (Russulales, Basidiomycota) are poorly known. Currently used classification systems still largely reflect the traditional, mainly morphological, characters used for infrageneric delimitations of milkcaps. Increased sampling, combined with small-scale molecular studies, show that this genus is underexplored and in need of revision. For this study, we assembled an extensive dataset of the genus Lactifluus, comprising 80 % of all known species and 30 % of the type collections. To unravel the infrageneric relationships within this genus, we combined a multi-gene molecular phylogeny, based on nuclear ITS, LSU, RPB2 and RPB1, with a morphological study, focussing on five important characteristics (fruit body type, presence of a secondary velum, colour reaction of the latex/context, pileipellis type and presence of true cystidia). Lactifluus comprises four supported subgenera, each containing several supported clades. With extensive sampling, ten new clades and at least 17 new species were discovered, which highlight the high diversity in this genus. The traditional infrageneric classification is only partly maintained and nomenclatural changes are proposed. Our morphological study shows that the five featured characteristics are important at different evolutionary levels, but further characteristics need to be studied to find morphological support for each clade. This study paves the way for a more detailed investigation of biogeographical history and character evolution within Lactifluus.
Regulation of an Escherichia coli/Mammalian Chimeric Carbamoyl-phosphate Synthetase*

Carbamoyl-phosphate synthetase (CPSase) consists of a 120-kDa synthetase domain (CPS) that makes carbamoyl phosphate from ATP, bicarbonate, and ammonia usually produced by a separate glutaminase domain. CPS is composed of two subdomains, CPS.A and CPS.B. Although CPS.A and CPS.B have specialized functions in intact CPSase, the separately cloned subdomains can catalyze carbamoyl phosphate synthesis. This report describes the construction of a 58-kDa chimeric CPSase composed of Escherichia coli CPS.A catalytic subdomains and the mammalian regulatory subdomain. The catalytic parameters are similar to those of the E. coli enzyme, but the activity is regulated by the mammalian effectors and protein kinase A phosphorylation. The chimera has a single site that binds phosphoribosyl 5′-pyrophosphate (PRPP) with a dissociation constant of 25 μm. The dissociation constant for UTP of 0.23 mm was inferred from its effect on PRPP binding. Thus, the regulatory subdomain is an exchangeable ligand binding module that can control both CPS.A and CPS.B domains, and the pathway for allosteric signal transmission is identical in E. coli and mammalian CPSase. A deletion mutant that truncates the polypeptide within a postulated regulatory sequence is as active as the parent chimera but is insensitive to effectors. PRPP and UTP bind to the mutant, suggesting that the carboxyl half of the subdomain is essential for transmitting the allosteric signal but not for ligand binding.
The role of trapped bubbles in kidney stone detection with the color Doppler ultrasound twinkling artifact

The color Doppler ultrasound twinkling artifact, which highlights kidney stones with rapidly changing color, has the potential to improve stone detection; however, its inconsistent appearance has limited its clinical utility. Recently, it was proposed stable crevice bubbles on the kidney stone surface cause twinkling; however, the hypothesis is not fully accepted because the bubbles have not been directly observed. In this paper, the micron or submicron-sized bubbles predicted by the crevice bubble hypothesis are enlarged in kidney stones of five primary compositions by exposure to acoustic rarefaction pulses or hypobaric static pressures in order to simultaneously capture their appearance by high-speed photography and ultrasound imaging. On filming stones that twinkle, consecutive rarefaction pulses from a lithotripter caused some bubbles to reproducibly grow from specific locations on the stone surface, suggesting the presence of pre-existing crevice bubbles. Hyperbaric and hypobaric static pressures were found to modify the twinkling artifact; however, the simple expectation that hyperbaric exposures reduce and hypobaric pressures increase twinkling by shrinking and enlarging bubbles, respectively, largely held for rough-surfaced stones but was inadequate for smoother stones. Twinkling was found to increase or decrease in response to elevated static pressure on smooth stones, perhaps because of the compression of internal voids. These results support the crevice bubble hypothesis of twinkling and suggest the kidney stone crevices that give rise to the twinkling phenomenon may be internal as well as external.