nifH diversity associated with Montastraea cavernosa identified using an optimized primer protocol

The diversity of nitrogen fixing bacteria in any system must be identified to in order to fully understand their ecological role. PCR is commonly used to investigate bacterial diversity. To capture the full diversity PCR primers must bind to and amplify all targeted DNA sequences. For this study I analyzed published universal nifH primers\u27 ability to capture the full diversity of nitrogen fixing bacteria. Based on this work I developed a new protocol for capturing the full diversity of nifH sequences. Using this optimized protocol I investigated community differences in nitrogen fixing bacteria between orange and brown color morphs of the Caribbean coral Montastraea cavernosa among three geographic locations. Whole community analysis revealed no difference between morphs or location. However, specific groups of proteobacteria and cyanobacteria differed in abundance between the morphs, indicating specific bacterial groups are responsible for differences previously observed in fixation between color morphs

Assessing 16S rRNA Marker-Gene Survey Measurement Process Using Mixtures of Environmental Samples

Microbial communities play a fundamental role in environmental and human health. Targeted sequencing of the 16S rRNA gene, 16S rRNA marker-gene surveys, is used to measure and thus characterize these communities. The 16S rRNA marker- gene survey measurement process includes a number of molecular laboratory and computational steps. A rigorous measurement assessment framework can evaluate measurement method performance, in turn improving the validity of marker-gene survey study conclusions. In this dissertation, I present a novel framework and mixture dataset for assessing 16S rRNA marker-gene survey bioinformatic methods. Additionally, I developed software to facilitate working with 16S rRNA reference sequence databases and 16S rRNA marker-gene survey feature data. Computational steps, collectively referred to as bioinformatic pipelines, combine multiple algorithms to convert raw sequence data into a count table, which is subsequently used to test biological hypotheses. Algorithm choice and parameters can significantly impact pipeline results. The assessment framework and software developed for this dissertation improve upon existing assessment methods and can be used to evaluate new computational methods and optimize existing pipelines. Furthermore, the assessment framework presented here can be applied to other microbial community measurement methods such as shotgun metagenomics

A measurement system for large, complex software programs

This paper describes measurement systems required to forecast, measure, and control activities for large, complex software development and support programs. Initial software cost and quality analysis provides the foundation for meaningful management decisions as a project evolves. In modeling the cost and quality of software systems, the relationship between the functionality, quality, cost, and schedule of the product must be considered. This explicit relationship is dictated by the criticality of the software being developed. This balance between cost and quality is a viable software engineering trade-off throughout the life cycle. Therefore, the ability to accurately estimate the cost and quality of software systems is essential to providing reliable software on time and within budget. Software cost models relate the product error rate to the percent of the project labor that is required for independent verification and validation. The criticality of the software determines which cost model is used to estimate the labor required to develop the software. Software quality models yield an expected error discovery rate based on the software size, criticality, software development environment, and the level of competence of the project and developers with respect to the processes being employed

Różnice wartości zautomatyzowanej pupilometrii służą jako wskaźnik prognostyczny, nawet gdy mieszczą się w normalnym zakresie

Introduction. The pupillary light reflex (PLR) is an integral aspect of the neurologic exam. With the enhancement of automated infrared pupillometry (AIP), the Neurological Pupil index (NPi) is being increasingly used when performing a neurological examination. NPi difference (the absolute difference between paired NPi readings from the left and right eye) is a relatively unexplored variable in AIP assessment.Aim. This study evaluates the association between Glasgow Coma Scale (GCS) scores and NPi differences between the left and right eyes, when the NPi is normal, in patients enrolled in a multi-center prospective database.Material and Methods. Restricting observations to only include NPi values ≥ 3 (normal), there were 2,572 qualifying patients with 3,519 pupillometer readings linked to GCS values. Linear regression and ANOVA models were developed to investigate the relationship between GCS and NPi difference.Results. Subject mean age was 55.88 (16.95) years and 54.5% were female. Mean NPi difference was 0.36 and mean GCS was 12.06. Regression analysis indicated a slight negative association between NPi difference and GCS (r2 = 0.0696, P < .0001). When observations were dichotomized as either NPi difference ≥ 0.7 (large) or < 0.7 (small), there was a statistically significant difference in the mean GCS (10.76 [3.90]) for large NPi difference vs. small NPi difference (13.15 [2.68]; P < .0001).Conclusions. Even among patients with normal PLR, a large NPi difference is associated with lower GCS scores. Trending and evaluating the NPi difference may become an important aspect of patient assessment. (JNNN 2021;10(4):168–174)Wstęp. Odruch źreniczny na światło (PLR) jest integralną częścią badania neurologicznego. Wraz z udoskonaleniem automatycznej pupilometrii w podczerwieni (AIP), wskaźnik neurologiczny źrenicy (NPi) jest coraz częściej używany podczas wykonywania badań neurologicznych. Różnica NPi (bezwzględna różnica między sparowanymi odczytami NPi z lewego i prawego oka) jest stosunkowo niezbadaną zmienną w ocenie AIP.Cel. Niniejsze badanie ocenia związek między wynikami w skali Glasgow (GCS) a różnicami NPi między lewym i prawym okiem, gdy NPi jest prawidłowe, u pacjentów włączonych do wieloośrodkowej prospektywnej bazy danych.Materiał i metody. Ograniczając obserwacje tylko do wartości NPi ≥ 3 (normalne), zakwalifikowano 2572 pacjentów z 3519 odczytami z pupilometru powiązanymi z wartościami GCS. Opracowano modele regresji liniowej i ANOVA w celu zbadania związku między różnicami między GCS a NPi.Wyniki. Średnia wieku badanych wynosiła 55,88 (16,95) lat i 54,5% stanowiły kobiety. Średnia różnica NPi wynosiła 0,36, a średnia GCS 12,06. Analiza regresji wykazała niewielki negatywny związek między różnicą NPi a GCS (r2 = 0,0696, P < 0,0001). Gdy obserwacje zostały rozdzielone jako różnica NPi ≥ 0,7 (duża) lub < 0,7 (mała), wystąpiła statystycznie istotna różnica w średniej GCS (10,76 [3,90]) dla dużej różnicy NPi vs małej różnicy NPi (13,15 [2,68]); P < 0,0001).Wnioski. Nawet wśród pacjentów z prawidłowym PLR duża różnica w NPi wiąże się z niższymi wynikami GCS. Trendy i ocena różnicy NPi mogą stać się ważnym aspektem oceny pacjenta. (PNN 2021;10(4):168–174

Emergency Medicine In-Training Examination Scores are Not Associated with Burnout and Not Affected by the Introduction of a Wellness Curriculum

Introduction: There is little research examining the relationship between burnout and medical knowledge. Study Objectives: The authors sought to determine if emergency medicine (EM) resident performance on the In-Training Examination (EM-ITE) is associated with burnout and if EM-ITE scores are affected by the implementation of a wellness curriculum. Methods: As part of a multi-institution prospective education intervention trial, the Maslach Burnout Inventory, a valuable tool in the assessment of physician burnout, was administered at 10 EM residencies in February 2017. Then, five intervention sites introduced a year-long wellness curriculum. The MBI was re-administered at all sites in August 2017 and February 2018. The EM-ITE, an instrument for medical knowledge assessment, was administered in February 2017 and February 2018 at all sites. Results: 285/382 (75%) residents participated in the February 2017 data collection; 247/386 (64%) participated in August 2017; and 228/386 (59%) participated in February 2018. EM-ITE scores were reported for 296/383 (77.5%) residents for 2017 and 304/386 (78.8%) residents for 2018. There was no association between change in mean EM-ITE scores at the intervention sites compared to the control sites. In the subset of 172 residents who completed the 2017 and 2018 MBI, there was no correlation between burnout and changes in EM-ITE scores. Conclusion: In this study of EM residents, burnout was not associated with resident medical knowledge acquisition and change in EM resident medical knowledge was not affected by the introduction of a wellness curriculum

DNA cyclization and looping in the wormlike limit: normal modes and the validity of the harmonic approximation

For much of the last three decades Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, $J$, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last ten years, however, approaches based on harmonic analysis of semi-flexible polymer models have been introduced, which offer much greater computational efficiency than Monte Carlo techniques. These methods consider the ensemble of molecular conformations in terms of harmonic fluctuations about a well-defined elastic-energy minimum. However, the harmonic approximation is only applicable for small systems, because the accessible conformation space of larger systems is increasingly dominated by anharmonic contributions. In the case of computed values of the J factor, deviations of the harmonic approximation from the exact value of $J$ as a function of DNA length have not been characterized. Using a recent, numerically exact method that accounts for both anharmonic and harmonic contributions to $J$ for wormlike chains of arbitrary size, we report here the apparent error that results from neglecting anharmonic behavior. For wormlike chains having contour lengths less than four times the persistence length the error in $J$ arising from the harmonic approximation is generally small, amounting to free energies less than the thermal energy, $k_B T$. For larger systems, however, the deviations between harmonic and exact $J$ values increase approximately linearly with size.Comment: 23 pages, 6 figures. Typos corrected. Manuscript improve

Maxillomandibular Advancement in the Management of Obstructive Sleep Apnea

Maxillomandibular advancement (MMA) is a surgical option for obstructive sleep apnea (OSA). MMA involves forward-fixing the maxilla and mandible approximately 10  mm via Le Fort I maxillary and sagittal split mandibular osteotomies. We retrospectively reviewed outcomes from 24 consecutive OSA patients who underwent MMA at our institution. MMA resulted in an 83% reduction in the group mean apnea-hypopnea index (AHI) per polysomnography an average of 6.7 months after surgery. Forty-two percent of patients achieved a post-MMA AHI of less than 5 events/hour sleep and 71% achieved an AHI less than or equal to 10 events/hour sleep. The Epworth Sleepiness Scale score decreased by an average of 5 post-surgery. No parameters predictive of cure for OSA by MMA were identified

Rola zarejestrowanej objętości wyrzutu płynu mózgowo-rdzeniowego w przewidywaniu wyniku w zmodyfikowanej skali Rankina przy wypisie ze szpitala u pacjentów z krwawieniami podpajęczynówkowymi (DROPSS)

Introduction. External ventricular drain (EVD) placement is common among aneurysmal subarachnoid hemorrhage (aSAH). Draining cerebrospinal fluid (CSF) from the EVD is also common, yet little is known about how much to drain, the length of time to drain, or how drainage impacts patient outcomes. Aim. The purpose of this study is to correlate amount of CSF drainage to patient outcomes, via modified Rankin Score (mRS). Material and Methods. This retrospective review of data located in a local hospital-based registry and electronic medical record. A linear mixed effects model was constructed to examine CSF drainage volume as a predictor of mRS at discharge. Results. Data from 82 patients was included in this analysis. There was no statistically significant relationship between CSF totals and mRS at hospital discharge (p = 0.3614, r² = 0.01). After controlling for age, Hunt and Hess score, and subject as random effect, there was still no significant relationship between CSF drained and mRS score at hospital discharge (p = .9042). Conclusions. There is no correlation between the total volume of CSF drained and mRS at discharge. Future research should explore CSF drainage documentation practices. (JNNN 2022;11(2):43–48) Key Words: acute care, aneurysmal subarachnoid hemorrhage, cerebrospinal fluid, external ventricular drain, patient outcomesWstęp. Założenie drenu komorowego zewnętrznego (EVD) jest powszechne w przypadku tętniakowatego krwotoku podpajęczynówkowego (aSAH). Drenaż płynu mózgowo-rdzeniowego (cerebrospinal fluid, CSF) z EVD jest również powszechny, jednak niewiele wiadomo na temat ilości płynu, czasu trwania drenażu i wpływu drenażu na wyniki leczenia. Cel. Celem tego badania jest korelacja ilości drenażu płynu mózgowo-rdzeniowego z wynikami leczenia pacjentów w zmodyfikowanej skali Rankina (modified Rankin Score, mRS). Materiał i metody. Retrospektywny przegląd danych znajdujących się w lokalnym rejestrze szpitalnym i elektronicznej dokumentacji medycznej. W celu zbadania objętości drenażu płynu mózgowo-rdzeniowego jako predyktora mRS przy wypisie ze szpitala skonstruowano liniowy model efektów mieszanych. Wyniki. Do analizy włączono dane od 82 pacjentów. Nie stwierdzono istotnej statystycznie zależności między całkowitą objętością płynu mózgowo-rdzeniowego a mRS przy wypisie ze szpitala (p = 0,3614, r² = 0,01). Po uwzględnieniu wieku, punktacji w skali Hunta i Hessa oraz podmiotu jako efektu losowego, nadal nie było istotnej zależności między odsączonym płynem mózgowo-rdzeniowym a wynikiem mRS przy wypisie ze szpitala (p = .9042). Wnioski. Nie ma korelacji między całkowitą objętością zdrenowanego płynu mózgowo-rdzeniowego a mRS przy wypisie ze szpitala. W przyszłych badaniach należy przeanalizować sposób prowadzenia dokumentacji drenażu płynu mózgowo-rdzeniowego. (PNN 2022;11(2):43–48)