Reaping the Harvest: Developing the Idaho Harvester

Social media platforms like Tumblr offer a quick, easy, and popular way for archives to conduct outreach and engage users with collections without requiring technical expertise like computer programming and web design. However, as the University of Idaho Library, Special Collections and Archives Department discovered after years of using Tumblr for online outreach, there are significant disadvantages to using a third-party social media platform. Unable to control the discoverability, display, and preservation of blog posts, it became clear that Tumblr was no longer serving the department’s evolving needs, necessitating an alternative solution moving forward. Special Collections & Archives partnered with the library’s Data and Digital Services Department to develop a custom self-hosted platform for sharing archival collections and staff institutional knowledge. This platform, the Idaho Harvester, combines the useful functions of a blog with those of a digital collection to ensure the digitization and research conducted for outreach is easily discoverable and effectively preserved. This article describes the disadvantages of a third-party social media platform for archival outreach and the benefits of a self-hosted platform like the Idaho Harvester to demonstrate the need for a multi-platform approach to online archival outreach. Although working with a self-hosted platform like the Idaho Harvester requires more technical skills than working with a social media platform like Tumblr, we argue that it meets the goals of discoverability, display, and preservation better than Tumblr or other social media platforms. As archival work becomes increasingly digital, this case study serves as an example of how archival outreach demands have evolved over time and how to assess online outreach tools and develop a multi-platform approach that works for archives’ unique and evolving needs

Association of operative approach with postoperative outcomes in neonates undergoing surgical repair of esophageal atresia and tracheoesophageal fistula

Introduction: Minimally invasive surgery (MIS) is gaining traction as a first-line approach to repair congenital anomalies. This study aims to evaluate outcomes for neonates undergoing open versus MIS repairs for esophageal atresia/tracheoesophageal fistula (EA/TEF). Methods: Neonates undergoing EA/TEF repair from 2013-2020 were identified using the National Surgical Quality Improvement Program-Pediatric database. Proportions of operative approach (open vs. MIS) over time were analyzed. A propensity score-matched analysis using preoperative characteristics was performed and outcomes were compared including composite morbidity and reintervention rates (overall, major [thoracoscopy, thoracotomy], and minor [chest/feeding tube placement, endoscopy]) between operative approaches. Pearson’s chi-square or Fisher’s exact test were used as appropriate. Results: We identified 1738 neonates who underwent EA/TEF repair. MIS utilization increased over time (p=0.019). Pre-match, neonates undergoing open repair were more likely premature, lower weight, and higher ASA class. Post-match, the groups were similar and included 183 neonates per group. MIS repair was associated with longer median operative time (206 vs. 180 minutes, p\u3c0.001), increased overall reintervention rates (MIS 9.8% vs. open 3.3%, p=0.011), and increased minor reintervention rates (MIS 7.7% vs. open 2.2%, p=0.016). There were no differences in composite morbidity (MIS 20.2% vs. open 26.8%, p=0.14) or major reinterventions (MIS 2.2% vs. open 1.1%, p=0.41). Discussion: MIS is gaining traction as a first-line approach for neonates with EA/TEF but appears to be associated with a higher rate of reinterventions. Further studies evaluating MIS approaches for the repair of EA/TEF are needed to better define short and long-term outcomes to optimize patient selection

Minimally Invasive Surgery in Neonates with Congenital Anomalies: Experience from the NSQIP-P

Background: Congenital diaphragmatic hernias (CDH) and tracheoesophageal fistulas (TEF) are managed with minimally invasive surgery (MIS) or open surgery. Little is known about the patient populations and outcomes for those treated by each approach. Hypothesis/Specific Aims: We expect that there will be fewer complications, better outcomes, and longer operative times for the MIS group versus the open group. Methods: National Surgical Quality Improvement Program-Pediatric Participant Use Files (NSQIP-P PUFs) from 2012-2015 were used to identify neonates (up to 30 days old) who underwent CDH and TEF repair. The patient characteristics, post-operative complications, and 30-day mortality were analyzed using multivariable logistic regression to determine morbidity associated with each. Data/Results: We identified 1,142 neonates who underwent CDH (n=577) and TEF (n=565) repair. Neonates who underwent open repair were sicker than those who underwent MIS and had slightly worse select outcomes. Median operative time was longer for both CDH and TEF with the MIS approach. However, multivariable logistic regression analysis adjusting for patient comorbidities showed that open versus MIS surgical approach was not associated with increased morbidity. Discussion: Neonates who underwent MIS repair had fewer co-morbidities and better outcomes. This surgical approach was not associated with any adverse 30-day outcomes in the multivariable models. This suggests that MIS repair of CDH and TEF can be safely performed in a subset of patients, but further research is needed to understand whether surgical approach affects the incidence of longer-term complications such as CDH recurrence or esophageal stricture

Genome-scale resources for Thermoanaerobacterium saccharolyticum

Background Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation. Results Here we present a set of genome-scale resources to enable the systems level investigation and development of this potentially important industrial organism. Resources include a complete genome sequence for strain JW/SL-YS485, a genome-scale reconstruction of metabolism, tiled microarray data showing transcription units, mRNA expression data from 71 different growth conditions or timepoints and GC/MS-based metabolite analysis data from 42 different conditions or timepoints. Growth conditions include hemicellulose hydrolysate, the inhibitors HMF, furfural, diamide, and ethanol, as well as high levels of cellulose, xylose, cellobiose or maltodextrin. The genome consists of a 2.7 Mbp chromosome and a 110 Kbp megaplasmid. An active prophage was also detected, and the expression levels of CRISPR genes were observed to increase in association with those of the phage. Hemicellulose hydrolysate elicited a response of carbohydrate transport and catabolism genes, as well as poorly characterized genes suggesting a redox challenge. In some conditions, a time series of combined transcription and metabolite measurements were made to allow careful study of microbial physiology under process conditions. As a demonstration of the potential utility of the metabolic reconstruction, the OptKnock algorithm was used to predict a set of gene knockouts that maximize growth-coupled ethanol production. The predictions validated intuitive strain designs and matched previous experimental results. Conclusion These data will be a useful asset for efforts to develop T. saccharolyticum for efficient industrial production of biofuels. The resources presented herein may also be useful on a comparative basis for development of other lignocellulose degrading microbes, such as Clostridium thermocellum. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0159-x) contains supplementary material, which is available to authorized users

The TESS-Keck Survey. XI. Mass Measurements for Four Transiting sub-Neptunes orbiting K dwarf TOI-1246

Multi-planet systems are valuable arenas for investigating exoplanet architectures and comparing planetary siblings. TOI-1246 is one such system, with a moderately bright K dwarf (V=11.6, K=9.9) and four transiting sub-Neptunes identified by TESS with orbital periods of 4.31 d, 5.90 d, 18.66 d, and 37.92 d. We collected 130 radial velocity observations with Keck/HIRES and TNG/HARPS-N to measure planet masses. We refit the 14 sectors of TESS photometry to refine planet radii (2.97±0.06 R⊕,2.47±0.08 R⊕,3.46±0.09 R⊕, 3.72±0.16 R⊕), and confirm the four planets. We find that TOI-1246 e is substantially more massive than the three inner planets (8.1±1.1M⊕, 8.8±1.2M⊕, 5.3±1.7M⊕, 14.8±2.3M⊕). The two outer planets, TOI-1246 d and TOI-1246 e, lie near to the 2:1 resonance (Pe/Pd=2.03) and exhibit transit timing variations. TOI-1246 is one of the brightest four-planet systems, making it amenable for continued observations. It is one of only six systems with measured masses and radii for all four transiting planets. The planet densities range from 0.70±0.24 to 3.21±0.44g/cm3, implying a range of bulk and atmospheric compositions. We also report a fifth planet candidate found in the RV data with a minimum mass of 25.6 ± 3.6 M⊕. This planet candidate is exterior to TOI-1246 e with a candidate period of 93.8 d, and we discuss the implications if it is confirmed to be planetary in nature

The TESS-Keck Survey. XI. Mass Measurements for Four Transiting Sub-Neptunes Orbiting K Dwarf TOI-1246

Multiplanet systems are valuable arenas for investigating exoplanet architectures and comparing planetary siblings. TOI-1246 is one such system, with a moderately bright K dwarf (V = 11.6, K = 9.9) and four transiting sub-Neptunes identified by TESS with orbital periods of 4.31, 5.90, 18.66, and 37.92 days. We collected 130 radial velocity observations with Keck/HIRES and TNG/HARPS-N to measure planet masses. We refit the 14 sectors of TESS photometry to refine planet radii (2.97 +/- 0.06 R (circle plus), 2.47 +/- 0.08 R (circle plus), 3.46 +/- 0.09 R (circle plus), and 3.72 +/- 0.16 R (circle plus)) and confirm the four planets. We find that TOI-1246 e is substantially more massive than the three inner planets (8.1 +/- 1.1 M (circle plus), 8.8 +/- 1.2 M (circle plus), 5.3 +/- 1.7 M (circle plus), and 14.8 +/- 2.3 M (circle plus)). The two outer planets, TOI-1246 d and TOI-1246 e, lie near to the 2:1 resonance (P (e)/P ( d ) = 2.03) and exhibit transit-timing variations. TOI-1246 is one of the brightest four-planet systems, making it amenable for continued observations. It is one of only five systems with measured masses and radii for all four transiting planets. The planet densities range from 0.70 +/- 0.24 to 3.21 +/- 0.44 g cm(-3), implying a range of bulk and atmospheric compositions. We also report a fifth planet candidate found in the RV data with a minimum mass of 25.6 +/- 3.6 M (circle plus). This planet candidate is exterior to TOI-1246 e, with a candidate period of 93.8 days, and we discuss the implications if it is confirmed to be planetary in nature

An assessment of prevalence of Type 1 CFI rare variants in European AMD, and why lack of broader genetic data hinders development of new treatments and healthcare access

PurposeAdvanced age-related macular degeneration (AAMD) risk is associated with rare complement Factor I (FI) genetic variants associated with low FI protein levels (termed ‘Type 1’), but it is unclear how variant prevalences differ between AMD patients from different ethnicities.MethodsCollective prevalence of Type 1 CFI rare variant genotypes were examined in four European AAMD datasets. Collective minor allele frequencies (MAFs) were sourced from the natural history study SCOPE, the UK Biobank, the International AMD Genomics Consortium (IAMDGC), and the Finnish Biobank Cooperative (FINBB), and compared to paired control MAFs or background population prevalence rates from the Genome Aggregation Database (gnomAD). Due to a lack of available genetic data in non-European AAMD, power calculations were undertaken to estimate the AAMD population sizes required to identify statistically significant association between Type 1 CFI rare variants and disease risk in different ethnicities, using gnomAD populations as controls.ResultsType 1 CFI rare variants were enriched in all European AAMD cohorts, with odds ratios (ORs) ranging between 3.1 and 7.8, and a greater enrichment was observed in dry AMD from FINBB (OR 8.9, 95% CI 1.49–53.31). The lack of available non-European AAMD datasets prevented us exploring this relationship more globally, however a statistical association may be detectable by future sequencing studies that sample approximately 2,000 AAMD individuals from Ashkenazi Jewish and Latino/Admixed American ethnicities.ConclusionsThe relationship between Type 1 CFI rare variants increasing odds of AAMD are well established in Europeans, however the lack of broader genetic data in AAMD has adverse implications for clinical development and future commercialisation strategies of targeted FI therapies in AAMD. These findings emphasise the importance of generating more diverse genetic data in AAMD to improve equity of access to new treatments and address the bias in health care.</p