Molecular mechanism for the interaction between human CPSF30 and hFip1.

Most eukaryotic pre-mRNAs must undergo 3'-end cleavage and polyadenylation prior to their export from the nucleus. A large number of proteins in several complexes participate in this 3'-end processing, including cleavage and polyadenylation specificity factor (CPSF) in mammals. The CPSF30 subunit contains five CCCH zinc fingers (ZFs), with ZF2-ZF3 being required for the recognition of the AAUAAA poly(A) signal. ZF4-ZF5 recruits the hFip1 subunit of CPSF, although the details of this interaction have not been characterized. Here we report the crystal structure of human CPSF30 ZF4-ZF5 in complex with residues 161-200 of hFip1 at 1.9 Å resolution, illuminating the molecular basis for their interaction. Unexpectedly, the structure reveals one hFip1 molecule binding to each ZF4 and ZF5, with a conserved mode of interaction. Our mutagenesis studies confirm that the CPSF30-hFip1 complex has 1:2 stoichiometry in vitro. Mutation of each binding site in CPSF30 still allows one copy of hFip1 to bind, while mutation of both sites abrogates binding. Our fluorescence polarization binding assays show that ZF4 has higher affinity for hFip1, with a Kd of 1.8 nM. We also demonstrate that two copies of the catalytic module of poly(A) polymerase (PAP) are recruited by the CPSF30-hFip1 complex in vitro, and both hFip1 binding sites in CPSF30 can support polyadenylation.

An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11.

Human cleavage and polyadenylation specificity factor (CPSF)73 (also known as CPSF3) is the endoribonuclease that catalyzes the cleavage reaction for the 3'-end processing of pre-mRNAs. The active site of CPSF73 is located at the interface between a metallo-ß-lactamase domain and a ß-CASP domain. Two metal ions are coordinated by conserved residues, five His and two Asp, in the active site, and they are critical for the nuclease reaction. The metal ions have long been thought to be zinc ions, but their exact identity has not been examined. Here we present evidence from inductively coupled plasma mass spectrometry and X-ray diffraction analyses that a mixture of metal ions, including Fe, Zn, and Mn, is present in the active site of CPSF73. The abundance of the various metal ions is different in samples prepared from different expression hosts. Zinc is present at less than 20% abundance in a sample expressed in insect cells, but the sample is active in cleaving a pre-mRNA substrate in a reconstituted canonical 3'-end processing machinery. Zinc is present at 75% abundance in a sample expressed in human cells, which has comparable endonuclease activity. We also observe a mixture of metal ions in the active site of the CPSF73 homolog INTS11, the endonuclease for Integrator. Taken together, our results provide further insights into the role of metal ions in the activity of CPSF73 and INTS11 for RNA 3'-end processing.

Antibiotic Prescribing Patterns for Respiratory Tract Illnesses Following the Conclusion of an Education and Feedback Intervention in Primary Care.

BACKGROUND: A study previously conducted in primary care practices found that implementation of an educational session and peer comparison feedback was associated with reduced antibiotic prescribing for respiratory tract diagnoses (RTDs). Here, we assess the long-term effects of this intervention on antibiotic prescribing following cessation of feedback. METHODS: RTD encounters were grouped into tiers based on antibiotic prescribing appropriateness: tier 1, almost always indicated; tier 2, possibly indicated; and tier 3, rarely indicated. A χ2 test was used to compare prescribing between 3 time periods: pre-intervention, intervention, and post-intervention (14 months following cessation of feedback). A mixed-effects multivariable logistic regression analysis was performed to assess the association between period and prescribing. RESULTS: We analyzed 260 900 RTD encounters from 29 practices. Antibiotic prescribing was more frequent in the post-intervention period than in the intervention period (28.9% vs 23.0%, P < .001) but remained lower than the 35.2% pre-intervention rate (P < .001). In multivariable analysis, the odds of prescribing were higher in the post-intervention period than the intervention period for tier 2 (odds ratio [OR], 1.19; 95% confidence interval [CI]: 1.10-1.30; P < .05) and tier 3 (OR, 1.20; 95% CI: 1.12-1.30) indications but was lower compared to the pre-intervention period for each tier (OR, 0.66; 95% CI: 0.59-0.73 tier 2; OR, 0.68; 95% CI: 0.61-0.75 tier 3). CONCLUSIONS: The intervention effects appeared to last beyond the intervention period. However, without ongoing provider feedback, there was a trend toward increased prescribing. Future studies are needed to determine optimal strategies to sustain intervention effects.

Parton Showering with Higher Logarithmic Accuracy for Soft Emissions.

The accuracy of parton-shower simulations is often a limiting factor in the interpretation of data from high-energy colliders. We present the first formulation of parton showers with accuracy 1 order beyond state-of-the-art next-to-leading logarithms, for classes of observables that are dominantly sensitive to low-energy (soft) emissions, specifically nonglobal observables and subjet multiplicities. This represents a major step toward general next-to-next-to-leading logarithmic accuracy for parton showers.

Improving Outpatient Antibiotic Prescribing for Respiratory Tract Infections in Primary Care: A Stepped-Wedge Cluster Randomized Trial.

BACKGROUND: Inappropriate antibiotic prescribing is common in primary care (PC), particularly for respiratory tract diagnoses (RTDs). However, the optimal approach for improving prescribing remains unknown. METHODS: We conducted a stepped-wedge study in PC practices within a health system to assess the impact of a provider-targeted intervention on antibiotic prescribing for RTDs. RTDs were grouped into tiers based on appropriateness of antibiotic prescribing: tier 1 (almost always indicated), tier 2 (may be indicated), and tier 3 (rarely indicated). Providers received education on appropriate RTD prescribing followed by monthly peer comparison feedback on antibiotic prescribing for (1) all tiers and (2) tier 3 RTDs. A χ 2 test was used to compare the proportion of visits with antibiotic prescriptions before and during the intervention. Mixed-effects multivariable logistic regression analysis was performed to assess the association between the intervention and antibiotic prescribing. RESULTS: Across 30 PC practices and 185 755 total visits, overall antibiotic prescribing was reduced with the intervention, from 35.2% to 23.0% of visits (P < .001). In multivariable analysis, the intervention was associated with a reduced odds of antibiotic prescription for tiers 2 (odds ratio [OR] 0.57; 95% confidence interval [CI] .52-.62) and 3 (OR 0.57; 95% CI .53-.61) but not for tier 1 (OR 0.98; 95% CI .83-1.16). CONCLUSIONS: A provider-focused intervention reduced overall antibiotic prescribing for RTDs without affecting prescribing for infections that likely require antibiotics. Future research should examine the sustainability of such interventions, potential unintended adverse effects on patient health or satisfaction, and provider perceptions and acceptability.

Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs.

We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5'caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins-Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.

Biophysical characterizations of the recognition of the AAUAAA polyadenylation signal.

Most eukaryotic messenger RNA precursors must undergo 3'-end cleavage and polyadenylation for maturation. We and others recently reported the structure of the AAUAAA polyadenylation signal (PAS) in complex with the protein factors CPSF-30, WDR33, and CPSF-160, revealing the molecular mechanism for this recognition. Here we have characterized in detail the interactions between the PAS RNA and the protein factors using fluorescence polarization experiments. Our studies show that AAUAAA is recognized with ∼3 nM affinity by the CPSF-160-WDR33-CPSF-30 ternary complex. Variations in the RNA sequence can greatly reduce the affinity. Similarly, mutations of CPSF-30 residues that have van der Waals interactions with the bases of AAUAAA also lead to substantial reductions in affinity. Finally, our studies confirm that both CPSF-30 and WDR33 are required for high-affinity binding of the PAS RNA, while these two proteins alone and their binary complexes with CPSF-160 have much lower affinity for the RNA.

Molecular basis for the recognition of the human AAUAAA polyadenylation signal.

Nearly all eukaryotic messenger RNA precursors must undergo cleavage and polyadenylation at their 3'-end for maturation. A crucial step in this process is the recognition of the AAUAAA polyadenylation signal (PAS), and the molecular mechanism of this recognition has been a long-standing problem. Here, we report the cryo-electron microscopy structure of a quaternary complex of human CPSF-160, WDR33, CPSF-30, and an AAUAAA RNA at 3.4-Å resolution. Strikingly, the AAUAAA PAS assumes an unusual conformation that allows this short motif to be bound directly by both CPSF-30 and WDR33. The A1 and A2 bases are recognized specifically by zinc finger 2 (ZF2) of CPSF-30 and the A4 and A5 bases by ZF3. Interestingly, the U3 and A6 bases form an intramolecular Hoogsteen base pair and directly contact WDR33. CPSF-160 functions as an essential scaffold and preorganizes CPSF-30 and WDR33 for high-affinity binding to AAUAAA. Our findings provide an elegant molecular explanation for how PAS sequences are recognized for mRNA 3'-end formation.

Impact of Reduced Preincision Antibiotic Infusion Time on Surgical Site Infection Rates: A Retrospective Cohort Study.

OBJECTIVE: Our objective was to determine the impact of total preincision infusion time on surgical site infections (SSIs) and establish an optimal time threshold for subsequent prospective study. BACKGROUND: SSIs remain a major cause of morbidity. Although regulated, the total time of infusion of preincision antibiotics varies widely. Impact of infusion time on SSI risk is poorly understood. METHODS: All consecutive patients (n = 46,791) undergoing inpatient surgical intervention were retrospectively enrolled (2014-2015) and monitored for 1 year. Primary outcomes: the presence of SSI infection as predicted by reduced preoperative antibiotic infusion time. SECONDARY OUTCOMES: preintervention compliance, the impact of a quality improvement algorithm to optimize infusion time compliance. Multivariate logistic regression of the retrospective cohort demonstrated predictors of infection. Receiver-operating characteristic analysis demonstrated the timing threshold predictive of infection. Cost impact of avoidable infections was analyzed. RESULTS: Only 36.1% of patients received preincision infusion of vancomycin in compliance with national and institutional standards (60-120 min). Cephalosporin infusion times were 53 times more likely to be compliant [odds ratio (OR) 53.33, P < 0.001]. Vancomycin infusion times that were not compliant with national standards (less than standard 60-120 min) did not predict infection. However, significantly noncompliant, reduced preincision infusion time, significantly predicted SSI (<24.6 min infusion, AUC = 0.762). Vancomycin infusion, initiated too close to surgical incision, predicted increased SSI (OR = 4.281, P < 0.001). Implementation of an algorithm to improve infusion time, but not powered to demonstrate infection /reduction, improved vancomycin infusion start time (257% improvement, P < 0.001) and eliminated high-risk infusions (sub-24.6 min). CONCLUSIONS: Initially, vancomycin infusion rarely met national guidelines; however, minimal compliance breach was not associated with SSI implications. The retrospective data here suggest a critical infusion time for infection reduction (24.6 min before incision). Prospective implementation of an algorithm led to 100% compliance. These data suggest that vancomycin administration timing should be studied prospectively.

Parton Showers beyond Leading Logarithmic Accuracy.

Parton showers are among the most widely used tools in collider physics. Despite their key importance, none so far have been able to demonstrate accuracy beyond a basic level known as leading logarithmic order, with ensuing limitations across a broad spectrum of physics applications. In this Letter, we propose criteria for showers to be considered next-to-leading logarithmic accurate. We then introduce new classes of shower, for final-state radiation, that satisfy the main elements of these criteria in the widely used large-N_{C} limit. As a proof of concept, we demonstrate these showers' agreement with all-order analytical next-to-leading logarithmic calculations for a range of observables, something never so far achieved for any parton shower.

Risk of invasive fungal infections in patients with high-risk MDS and AML receiving hypomethylating agents.

Invasive fungal infections (IFI) are a significant source of morbidity and mortality for patients with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). Given the heterogeneity of the population receiving hypomethylating agents (HMA), it is difficult for clinicians to accurately assess their patients' risk of infection. Literature on the incidence of IFI following HMA is limited to several studies of azacitidine. The primary objective of this retrospective study was to establish the incidence of IFI in HMA treated AML/MDS patients at a large U.S. comprehensive cancer center. Secondary objectives included comparing incidence of IFI among pre-specified subgroups to identify potential risk factors for IFI. Two hundred three patients with AML, intermediate to very high risk MDS or chronic myelomonocytic leukemia who received at least two cycles of HMA were included. The incidence of IFI, as defined by the European Organization for Research and Treatment of Cancer / Invasive Fungal Infections Cooperative Group criteria, was 9.6%, with 20 IFI diagnosed following HMA (three proven, four probable, 13 possible). Among the proven cases of IFI, molds included Scedosporium and Fusarium spp. Eleven patients who developed IFIs were neutropenic upon initiating HMA. The majority (17/20) of infections occurred during the first four cycles. Given this incidence, mold-active prophylaxis can be considered in patients who are neutropenic at the start of therapy.

Student and Institutional Achievements during an OIE Veterinary Education Twinning Project Collaboration between Sokoine University of Agriculture and Kansas State University.

This collaborative partnership aimed to enhance the quality of veterinary education at both Sokoine University of Agriculture (SUA), College of Veterinary Medicine and Biomedical Sciences (Tanzania), and Kansas State University (KSU), College of Veterinary Medicine (United States), by facilitating exchange of knowledge, experience, and ideas. One project objective was to integrate the World Organisation for Animal Health (OIE) Guidelines on Veterinary Education Core Curriculum into the SUA education program so veterinary graduates would be equipped with the minimum competencies needed to support their National Veterinary Services (OIE Day 1 Competencies). Curriculum mapping revealed that partners addressed different OIE Day 1 Competencies to varying degrees and they had complementary strengths and weaknesses. The partners' practical and educational experiences were also complementary, providing each opportunities to learn from the other and a solid basis for long-term mutually beneficial collaboration. Through structured exchanges, the collaboration allowed SUA and KSU students and faculty to broaden their perspectives by exposing them to veterinary medicine, culture, ecosystems, teaching environments, and farming systems in each other's country. Visiting faculties and students from both universities were exposed to different livestock systems, varying dynamics at the human-livestock-wildlife interface, different teaching systems, and a veterinary profession with a different culture and focus than that in their own country. Students and faculty learned about the relative social and economic importance of different types of animal production in each country and their influence on veterinary education priorities. Partnership outcomes include a continuing professional development course at SUA for private and public sector veterinarians and a clinical club to expose students at both colleges to a broader range of clinical cases and knowledge.

Evaluation of the Bachelor of Veterinary Medicine (BVM) Curriculum at Sokoine University of Agriculture in Tanzania: Mapping to OIE Veterinary Graduate 'Day 1 Competencies'.

The World Organisation for Animal Health (OIE) provides the requirements needed for graduating veterinary professionals to be competent in the delivery of animal health services. However, significant differences in veterinary curricula across countries-attributable to differing animal health priorities and predominant types of veterinary practice-provide a challenge for veterinary schools to address these competencies adequately. As part of the OIE's veterinary education establishment Twinning Project activities, the College of Veterinary Medicine and Biomedical Sciences (CVMBS) of Sokoine University of Agriculture (SUA) in Tanzania undertook a curriculum mapping and gap analysis to assess the extent to which the veterinary curriculum addresses OIE's 'Day 1 Competencies' for graduating veterinarians. Results of the analysis indicated that all the OIE's Day 1 Competencies (general, specific, and advanced) are addressed to some degree by the courses present in the curriculum. However, gaps in the depth and breadth of instruction were found for a number of competencies in all three categories. These findings indicate a need for addressing the gaps in the next curriculum review. This will allow the development of a stronger curriculum that will efficiently meet the national and international animal health requirements.

The Impact of Reported Beta-Lactam Allergy in Hospitalized Patients With Hematologic Malignancies Requiring Antibiotics.

Background: Patients hospitalized with hematologic malignancy are particularly vulnerable to infection. The impact of reported beta-lactam (BL) allergy in this population remains unknown. Methods: This was a retrospective cohort study of adult inpatients with hematologic malignancy admitted at 2 tertiary care hospitals from 2010 through 2015. The primary outcome was hospital length of stay (LOS) after administration of the first antibiotic. Secondary outcomes included readmission, mortality, complications, hospital charges, and antibiotic usage. Our goal was to define the impact of BL-only allergy (BLOA) label on clinical outcomes compared to those with no BL allergy (NBLA) in hematologic malignancy inpatients who required systemic antibiotics. Results: In our cohort (n = 4671), 38.3% had leukemia, 4.9% had Hodgkin lymphoma, 36.1% had non-Hodgkin lymphoma, and 20.7% had multiple myeloma. Among patients, 35.1% reported antibiotic allergy, and 14.1% (n = 660) had BLOA (including 9.3% with penicillin-only allergy and 3.3% cephalosporin-only allergy). Patients with BLOA had longer median LOS compared to patients with NBLA (11.3 vs 7.6 days, P < .001), which remained significant after multivariable adjustment. Patients with BLOA also had significantly worse outcomes in terms of mortality rate at 30 days (7.6% vs 5.3%, P = .017) and 180 days (15.8% vs 12.2%, P = .013), 30-day readmission rate, Clostridium difficile rate, hospital charges ($223 046 vs $173 256, P < .001), antibiotic classes used, and antibiotic duration. Conclusions: In hospitalized patients with hematologic malignancy, patients with reported BL allergy had worse clinical outcomes and higher healthcare cost than those without BL allergy label.

Antimicrobial Stewardship Training for Infectious Diseases Fellows: Program Directors Identify a Curriculum Need.

A needs assessment survey of infectious diseases (ID) training program directors identified gaps in educational resources for training and evaluating ID fellows in antimicrobial stewardship. An Infectious Diseases Society of America-sponsored core curriculum was developed to address that need.

The impact of infection among left ventricular assist device recipients on post-transplantation outcomes: A retrospective review.

INTRODUCTION: Left ventricular assist device (LVAD) infections are common, and the consequences of LVAD infections on orthotopic heart transplantation (OHT) outcomes are not well described. AIMS: The aim of this study was to describe clinical characteristics and evaluate risk factors for developing LVAD infections, and examine outcomes of LVAD-specific infections (VSI) after OHT. METHODS: We retrospectively investigated the records of 74 consecutive patients at two institutions who had undergone LVAD placement and subsequent OHT between January 2007 and December 2012. RESULTS: Forty-six of 74 (62%) LVAD recipients who underwent OHT had pre-transplant infections, and 18 (24%) had LVAD-specific infection (VSI), of which 71% were caused by gram-negative organisms. Of pre-transplant non-LVAD infections, Clostridium difficile infection (CDI) was the most common (26%) followed by urinary tract infection (UTI, 16%) and pneumonia (PNA 15%). Univariate analysis comparing subjects with VSI to those without VSI showed a significant association with time spent outside the hospital prior to transplantation (median 231.8 days vs 142.2 days, P < 0.03) and total time between VAD placement and OHT (244.0 days and 150.5 days, P < 0.002). Logistic regression was performed and significant predictors for VAD-related infection were age and the presence of diabetes, with type of device as an effect modifier. Six months post-OHT survival was not significantly affected by the presence of VSI prior to transplant. There was a trend toward an association between the presence of any infection and post-transplant rejection (P < 0.09). There were 10 post-transplant deaths by 6 months. Of these deaths, 4/10 (40%) were cardiopulmonary and 6/10 (60%) were related to infections. CONCLUSIONS: Advanced age and presence of diabetes were predictors of VSI, as well as type of VAD device, although device choice is likely affected by many clinical factors including age and comorbidities, as well as institution-specific preferences. VSI was not associated with a decrease in 6-month post-OHT survival. However, infections remain the major causes of death by 6 months post-transplant. Certain infections are associated with an increased risk of rejection, which merits further investigation.

Point-of-prescription interventions to improve antimicrobial stewardship.

Antimicrobial stewardship is pivotal to improving patient outcomes, reducing adverse events, decreasing healthcare costs, and preventing further emergence of antimicrobial resistance. In an era in which antimicrobial resistance is increasing, judicious antimicrobial use is the responsibility of every healthcare provider. Antimicrobial stewardship programs (ASPs) have made headway in improving antimicrobial prescribing using such "top-down" methods as formulary restriction and prospective audit with feedback; however, engagement of prescribers has not been fully explored. Strategies that include frontline prescribers and other unit-based healthcare providers have the potential to expand stewardship, both to augment existing centralized ASPs and to provide alternative approaches to perform stewardship at healthcare facilities with limited resources. This review discusses interventions focusing on antimicrobial prescribing at the point of prescription as well as a pilot project to engage unit-based healthcare providers in antimicrobial stewardship.

Identifying and Reducing Remaining Stocks of Rinderpest Virus.

In 2011, the world was declared free from rinderpest, one of the most feared and devastating infectious diseases of animals. Rinderpest is the second infectious disease, after smallpox, to have been eradicated. However, potentially infectious rinderpest virus material remains widely disseminated among research and diagnostic facilities across the world and poses a risk for disease recurrence should it be released. Member Countries of the World Organisation for Animal Health and the Food and Agricultural Organization of the United Nations are committed to destroying remaining stocks of infectious material or ensuring that it is stored under international supervision in a limited number of approved facilities. To facilitate this commitment and maintain global freedom from rinderpest, World Organisation for Animal Health Member Countries must report annually on rinderpest material held in their countries. The first official surveys, conducted during 2013-2015, revealed that rinderpest material was stored in an unacceptably high number of facilities and countries.