Rescue Allocation Modes in Eurotransplant Kidney Transplantation: Recipient Oriented Extended Allocation Versus Competitive Rescue Allocation-A Retrospective Multicenter Outcome Analysis

BACKGROUND

Whenever the kidney standard allocation (SA) algorithms according to the Eurotransplant (ET) Kidney Allocation System or the Eurotransplant Senior Program fail, rescue allocation (RA) is initiated. There are 2 procedurally different modes of RA: recipient oriented extended allocation (REAL) and competitive rescue allocation (CRA). The objective of this study was to evaluate the association of patient survival and graft failure with RA mode and whether or not it varied across the different ET countries.

METHODS

The ET database was retrospectively analyzed for donor and recipient clinical and demographic characteristics in association with graft outcomes of deceased donor renal transplantation (DDRT) across all ET countries and centers from 2014 to 2021 using Cox proportional hazards methods.

RESULTS

Seventeen thousand six hundred seventy-nine renal transplantations were included (SA 15 658 [89%], REAL 860 [4.9%], and CRA 1161 [6.6%]). In CRA, donors were older, cold ischemia times were longer, and HLA matches were worse in comparison with REAL and especially SA. Multivariable analyses showed comparable graft and recipient survival between SA and REAL; however, CRA was associated with shorter graft survival. Germany performed 76% of all DDRTs after REAL and CRA and the latter mode reduced waiting times by up to 2.9 y.

CONCLUSIONS

REAL and CRA are used differently in the ET countries according to national donor rates. Both RA schemes optimize graft utilization, lead to acceptable outcomes, and help to stabilize national DDRT programs, especially in Germany.

The scientific basis of 'net zero emissions' and its diverging sociopolitical representation

The Net Zero Emissions (NZE) concept has created momentum for climate commitment made by national governments, cities, industries and individual companies. However, evidence of tangible decarbonisation is limited. Here we identify precarious differences between the scientific origin of NZE and its social representation in the wider public and explore the consequences of the resulting science-action gap for achieving global climate goals. A particular focus is given to 'offsetting', which is closely connected to the practical delivery of NZE but typically ignores that different types or carbon credits have different environmental efficacy. Revisiting the science related to the global carbon cycle demonstrates that a heavy reliance on any carbon offsetting that is not a permanent removal presents a real risk. Moreover, competition over scarce 'removal credits' distracts from the real tasks at hand, namely to rapidly decrease fossil fuel emissions, actively remove carbon through restoration, and protect existing terrestrial carbon sinks. Establishing separate targets for these distinct actions is an essential step towards disentangling current confusion. Whilst a 'race to net zero' may trigger innovation in the decarbonisation space, the restoration and protection of carbon sinks demands a collective approach where actors should focus on how to make real and verifiable contributions rather than claiming individual net zero scores.

Diabetes, Obesity, and Pathological Upstaging in Renal Cell Carcinoma: Results From a Large Multi-institutional Consortium

PURPOSE

We sought to determine whether clinical risk factors and morphometric features on preoperative imaging can be utilized to identify those patients with cT1 tumors who are at higher risk of upstaging (pT3a).

MATERIALS AND METHODS

We performed a retrospective international case-control study of consecutive patients treated surgically with radical or partial nephrectomy for nonmetastatic renal cell carcinoma (cT1 N0) conducted between January 2010 and December 2018. Multivariable logistic regression models were used to study associations of preoperative risk factors on pT3a pathological upstaging among all patients, as well as subsets with those with preoperative tumors ≤4 cm, renal nephrometry scores, tumors ≤4 cm with nephrometry scores, and clear cell histology. We also examined association with pT3a subsets (renal vein, sinus fat, perinephric fat).

RESULTS

Among the 4,092 partial nephrectomy and 2,056 radical nephrectomy patients, pathological upstaging occurred in 4.9% and 23.3%, respectively. Among each group independent factors associated with pT3a upstaging were increasing preoperative tumor size, increasing age, and the presence of diabetes. Specifically, among partial nephrectomy subjects diabetes (OR=1.65; 95% CI 1.17, 2.29), male sex (OR=1.62; 95% CI 1.14, 2.33), and increasing BMI (OR=1.03; 95% CI 1.00, 1.05 per 1 unit BMI) were statistically associated with upstaging. Subset analyses identified hilar tumors as more likely to be upstaged (partial nephrectomy OR=1.91; 95% CI 1.12, 3.16; radical nephrectomy OR=2.16; 95% CI 1.44, 3.25).

CONCLUSIONS

Diabetes and higher BMI were associated with pathological upstaging, as were preoperative tumor size, increased age, and male sex. Similarly, hilar tumors were frequently upstaged.

Kidney Transplantation Outcome Predictions (KTOP): A Risk Prediction Tool for Kidney Transplants from Brain-dead Deceased Donors Based on a Large European Cohort

BACKGROUND

European kidney donation shortages mandate efficient organ allocation by optimizing the prediction of success for individual recipients.

OBJECTIVE

To develop the first European online risk tool for kidney transplant outcomes on the basis of recipient-only and recipient plus donor characteristics.

DESIGN, SETTING, AND PARTICIPANTS

We used individual recipient and donor risk factors and three outcomes (death, death with functioning graft [DWFG], and graft loss) for 32 958 transplants within the Eurotransplant kidney allocation system and the Eurotransplant senior program between January 2006 and May 2018 in eight European countries to develop and validate a risk tool.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Cox proportional-hazards models were used to analyze the association of risk factors with overall patient mortality, and proportional subdistribution hazard regression models for their association with graft loss and DWFG. Prediction models were developed with recipient-only and recipient-donor risk factors. Sensitivity analyses based on time-specific area under the receiver operating characteristic curve (AUC) with leave-one-country-out validation were performed and calibration plots were generated.

RESULTS AND LIMITATIONS

The 10-yr cumulative incidence rate was 37% for mortality, 12% for DWFG, and 41% for graft loss. In recipient-donor models the leading risk factors for mortality were recipient diabetes (hazard ratio [HR] 10.73), retransplantation (HR 3.08 per transplant), and recipient age (HR 1.08). Effects were similar for DWFG. For graft loss, diabetes (subdistributional HR [SHR] 1.32), increased donor age (SHR 1.02), and prolonged cold ischemia time (SHR 1.02) had increased SHRs. All p values were <0.001.

CONCLUSIONS

Previously identified risk factors for outcomes following kidney transplants allow for outcome prediction with 10-yr AUC values of up to 0.81.

PATIENT SUMMARY

Using European data, we estimated individual risks to predict the success of kidney transplants and support physicians in decision-making. An online tool is now available (https://riskcalc.org/ktop/) for predicting kidney transplant outcomes both before and after a donor has been identified.

Objective hearing threshold identification from auditory brainstem response measurements using supervised and self-supervised approaches

Hearing loss is a major health problem and psychological burden in humans. Mouse models offer a possibility to elucidate genes involved in the underlying developmental and pathophysiological mechanisms of hearing impairment. To this end, large-scale mouse phenotyping programs include auditory phenotyping of single-gene knockout mouse lines. Using the auditory brainstem response (ABR) procedure, the German Mouse Clinic and similar facilities worldwide have produced large, uniform data sets of averaged ABR raw data of mutant and wildtype mice. In the course of standard ABR analysis, hearing thresholds are assessed visually by trained staff from series of signal curves of increasing sound pressure level. This is time-consuming and prone to be biased by the reader as well as the graphical display quality and scale.In an attempt to reduce workload and improve quality and reproducibility, we developed and compared two methods for automated hearing threshold identification from averaged ABR raw data: a supervised approach involving two combined neural networks trained on human-generated labels and a self-supervised approach, which exploits the signal power spectrum and combines random forest sound level estimation with a piece-wise curve fitting algorithm for threshold finding.We show that both models work well and are suitable for fast, reliable, and unbiased hearing threshold detection and quality control. In a high-throughput mouse phenotyping environment, both methods perform well as part of an automated end-to-end screening pipeline to detect candidate genes for hearing involvement. Code for both models as well as data used for this work are freely available.

Association between short-term exposure to air pollution and COVID-19 mortality in all German districts: the importance of confounders

BACKGROUND

The focus of many studies is to estimate the effect of risk factors on outcomes, yet results may be dependent on the choice of other risk factors or potential confounders to include in a statistical model. For complex and unexplored systems, such as the COVID-19 spreading process, where a priori knowledge of potential confounders is lacking, data-driven empirical variable selection methods may be primarily utilized. Published studies often lack a sensitivity analysis as to how results depend on the choice of confounders in the model. This study showed variability in associations of short-term air pollution with COVID-19 mortality in Germany under multiple approaches accounting for confounders in statistical models.

METHODS

Associations between air pollution variables PM_2.5, PM₁₀, CO, NO, NO₂, and O₃ and cumulative COVID-19 deaths in 400 German districts were assessed via negative binomial models for two time periods, March 2020-February 2021 and March 2021-February 2022. Prevalent methods for adjustment of confounders were identified after a literature search, including change-in-estimate and information criteria approaches. The methods were compared to assess the impact on the association estimates of air pollution and COVID-19 mortality considering 37 potential confounders.

RESULTS

Univariate analyses showed significant negative associations with COVID-19 mortality for CO, NO, and NO₂, and positive associations, at least for the first time period, for O₃ and PM_2.5. However, these associations became non-significant when other risk factors were accounted for in the model, in particular after adjustment for mobility, political orientation, and age. Model estimates from most selection methods were similar to models including all risk factors.

CONCLUSION

Results highlight the importance of adequately accounting for high-impact confounders when analyzing associations of air pollution with COVID-19 and show that it can be of help to compare multiple selection approaches. This study showed how model selection processes can be performed using different methods in the context of high-dimensional and correlated covariates, when important confounders are not known a priori. Apparent associations between air pollution and COVID-19 mortality failed to reach significance when leading selection methods were used.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s12302-022-00657-5.

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.

Kidney Transplantation After Rescue Allocation-the Eurotransplant Experience: A Retrospective Multicenter Outcome Analysis

BACKGROUND

At Eurotransplant (ET), kidneys are transferred to "rescue allocation" (RA), whenever the standard allocation (SA) algorithms Eurotransplant Kidney Allocation System (ETKAS) and Eurotransplant Senior Program (ESP) fail. We analyzed the outcome of RA.

METHODS

Retrospective patient clinical and demographic characteristics association analyses were performed with graft outcomes for 2422 recipients of a deceased donor renal transplantation (DDRT) after RA versus 25 481 after SA from 71 centers across all ET countries from 2006 to 2018.

RESULTS

Numbers of DDRTs after RA increased over the time, especially in Germany. RA played a minor role in ESP versus ETKAS (2.7% versus 10.4%). RA recipients and donors were older compared with SA recipients and donors, cold ischemia times were longer, waiting times were shorter, and the incidence of primary nonfunction was comparable. Among ETKAS recipients, HLA matching was more favorable in SA (mean 3.7 versus 2.5). In multivariate modeling, the incidence of graft loss in ETKAS recipients was reduced in RA compared with SA (subdistribution hazard ratio, 0.80; 95% confidence interval [0.70-0.91], P < 0.001), whereas other outcomes (mortality, death with functioning graft (DwFG)) were not significantly different. None of the 3 outcomes were significantly different when comparing RA with SA within the ESP program.

CONCLUSIONS

Facing increased waiting times and mortality on dialysis due to donor shortage, this study reveals encouragingly positive DDRT outcomes following RA. This supports the extension of RA to more patients and as an alternative tool to enable transplantation in patients in countries with prohibitively long waiting times or at risk of deterioration.

Magseed localisation of non-palpable breast lesions: experience from a single centre

AIM

To prospectively analyse patients undergoing magnetic seed (Magseed) localisation (MSL) to evaluate the outcome, and to retrospectively compare re-excision rates for MSL with previous wire-guided localisation (WGL) to assess the hypothesis that the introduction of MSL may lead to a lower re-excision rate.

MATERIALS AND METHODS

MSL commenced at University Hospital Crosshouse in December 2017. No other changes were made to radiological or surgical practice during this time. Data were collected prospectively on all patients undergoing MSL between December 2017 and December 2019, in a single breast unit. Data were gathered retrospectively on patients who had undergone localised breast procedures between January 2016 and December 2019 for comparison of re-excision rates.

RESULTS

Two hundred and fifty-five patients underwent MSL surgery between December 2017 and December 2019. Of those, 98% (n=250) patients underwent successful MSL at the first attempt. The Magseed was identified intraoperatively in 100% patients and surgical excision was performed. The re-excision rate reduced from 18.9% in 2016/2017, to 11.6% in 2018/2019 (p=0.098).

CONCLUSION

In conclusion, Magseed localisation has proved to be a safe and effective way of localising breast lesions, with the advantage of high accuracy. The reduction in re-excision rates at University Hospital Crosshouse with the introduction of Magseed® localisation is a potential benefit, which requires further study.

Characterising a homozygous two-exon deletion in UQCRH: comparing human and mouse phenotypes

Mitochondrial disorders are clinically and genetically diverse, with isolated complex III (CIII) deficiency being relatively rare. Here, we describe two affected cousins, presenting with recurrent episodes of severe lactic acidosis, hyperammonaemia, hypoglycaemia and encephalopathy. Genetic investigations in both cases identified a homozygous deletion of exons 2 and 3 of UQCRH, which encodes a structural complex III (CIII) subunit. We generated a mouse model with the equivalent homozygous Uqcrh deletion (Uqcrh-/- ), which also presented with lactic acidosis and hyperammonaemia, but had a more severe, non-episodic phenotype, resulting in failure to thrive and early death. The biochemical phenotypes observed in patient and Uqcrh-/- mouse tissues were remarkably similar, displaying impaired CIII activity, decreased molecular weight of fully assembled holoenzyme and an increase of an unexpected large supercomplex (SXL ), comprising mostly of one complex I (CI) dimer and one CIII dimer. This phenotypic similarity along with lentiviral rescue experiments in patient fibroblasts verifies the pathogenicity of the shared genetic defect, demonstrating that the Uqcrh-/- mouse is a valuable model for future studies of human CIII deficiency.

SERENA: Particle Instrument Suite for Determining the Sun-Mercury Interaction from BepiColombo

The ESA-JAXA BepiColombo mission to Mercury will provide simultaneous measurements from two spacecraft, offering an unprecedented opportunity to investigate magnetospheric and exospheric particle dynamics at Mercury as well as their interactions with solar wind, solar radiation, and interplanetary dust. The particle instrument suite SERENA (Search for Exospheric Refilling and Emitted Natural Abundances) is flying in space on-board the BepiColombo Mercury Planetary Orbiter (MPO) and is the only instrument for ion and neutral particle detection aboard the MPO. It comprises four independent sensors: ELENA for neutral particle flow detection, Strofio for neutral gas detection, PICAM for planetary ions observations, and MIPA, mostly for solar wind ion measurements. SERENA is managed by a System Control Unit located inside the ELENA box. In the present paper the scientific goals of this suite are described, and then the four units are detailed, as well as their major features and calibration results. Finally, the SERENA operational activities are shown during the orbital path around Mercury, with also some reference to the activities planned during the long cruise phase.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density

The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease.

Patients affected by osteoporosis frequently present with decreased BMD and increased fracture risk. Genes are known to control the onset and progression of bone diseases such as osteoporosis. Therefore, we aimed to identify osteoporosis-related genes using BMD measures obtained from a large pool of mutant mice genetically modified for deletion of individual genes (knockout mice). In a collaborative endeavor involving several research sites world-wide, we generated and phenotyped 3,823 knockout mice and identified 200 genes which regulated BMD. Of the 200 BMD genes, 141 genes were previously not known to affect BMD. The discovery and study of novel BMD genes will help to better understand the causes and therapeutic options for patients with low BMD. In the long run, this will improve the clinical management of osteoporosis.

Dose-dependent long-term effects of a single radiation event on behaviour and glial cells

PURPOSE

The increasing use of low-dose ionizing radiation in medicine requires a systematic study of its long-term effects on the brain, behaviour and its possible association with neurodegenerative disease vulnerability. Therefore, we analysed the long-term effects of a single low-dose irradiation exposure at 10 weeks of age compared to medium and higher doses on locomotor, emotion-related and sensorimotor behaviour in mice as well as on hippocampal glial cell populations.

MATERIALS AND METHODS

We determined the influence of radiation dose (0, 0.063, 0.125 or 0.5 Gy), time post-irradiation (4, 12 and 18 months p.i.), sex and genotype (wild type versus mice with Ercc2 DNA repair gene point mutation) on behaviour.

RESULTS

The high dose (0.5 Gy) had early-onset adverse effects at 4 months p.i. on sensorimotor recruitment and late-onset negative locomotor effects at 12 and 18 months p.i. Notably, the low dose (0.063 Gy) produced no early effects but subtle late-onset (18 months) protective effects on sensorimotor recruitment and exploratory behaviour. Quantification and morphological characterization of the microglial and the astrocytic cells of the dentate gyrus 24 months p.i. indicated heightened immune activity after high dose irradiation (0.125 and 0.5 Gy) while conversely, low dose (0.063 Gy) induced more neuroprotective features.

CONCLUSION

This is one of the first studies demonstrating such long-term and late-onset effects on brain and behaviour after a single radiation event in adulthood.

Between Exploration, Pleasure, and Performance: Sexual Enhancement Medication Use among Older Gay and Heterosexual Men

Pharmaceutical marketing campaigns and biomedical discourses tend to oppose two types of sexual enhancement medication (SEM) use. While "therapeutic" use is associated with older heterosexual men in committed relationships, "recreational" use is associated with young gay men, and with the context of casual sex. However, little is known about the real objectives of older men (especially older gay men) who use SEM or the contexts in which they use such drugs. Furthermore, SEM conveys representations of masculinity and sexuality that focus on performance and youth, and the influence of these representations on SEM users remains unexplored. Based on semi-structured interviews conducted, in French, in 2015-2016, with 27 Canadian men (12 heterosexual, 15 gay) aged 65 to 84 years, we examined the context in which older men used such medication and the reasons why they used it, and we explored how older men's notions of sexuality, masculinity, and aging influenced their experiences with SEM use. Our participants' narratives focused on three themes: exploring sexual possibilities/improving one's sex life, restoring sexual capacities, and masculinity and aging. This study improves our understanding of older men's use of SEM and contributes to the deconstruction of normative models of older men's masculinity and sexuality.

Survival data on timing of resection of liver metastases in colorectal cancer patients

Between 2007 and 2016, 140 consecutive patients who underwent resection of colorectal cancer with simultaneous liver metastases at a single university hospital were retrospectively analysed. In order to gather information regarding potential survival differences for n = 68 simultaneous versus n = 72 staged resections of the colorectal primary tumor and the liver metastases, Clinical, histopathological, serological, and survival data were compared for those two patient groups. The rate of simultaneous tumor resections increased from approximately 25% in 2007 to >75% in 2016. There was no difference in tumor specific survival for patients with simultaneous vs. staged resection (p = 0.631). This effect continued after excluding patients with extrahepatic metastases (p = 0.440). Further, neoadjuvant treatment did not lead to differences in the tumor-specific survival (p = 0.123). Factors associated with an increased tumor-specific survival were low ASA score (p < 0.001), low number of tumor-affected lymph nodes (p < 0.001), histological grading G1/2 (p = 0.001), and a low number of liver metastases (p = 0.044). There was no significant survival difference for the primary tumor stage (pT), the Clavien-Dindo complication rate, the resection status (R0), and minor versus major hepatectomies.

Simultaneous Versus Staged Resection of Colorectal Cancer Liver Metastasis: A Retrospective Single-Center Study

BACKGROUND

For patients with colorectal cancer and synchronous liver metastasis, either a simultaneous, or a two-staged resection of the primary tumor and the liver metastases is possible. There are currently no guidelines preferring one approach to the other.

MATERIAL AND METHODS

Consecutive patients who underwent hepatic resection at our university hospital from 2007-2016 were included. Clinical, histopathologic, serologic, and survival data were analyzed. The primary end point was tumor-specific survival for patients with simultaneous versus staged resections.

RESULTS

Of all 140 patients, 68 underwent simultaneous resection and 72 underwent staged resection. The characteristics of both groups were comparable. Patients with simultaneous resections had a shorter duration of cumulative operation time (299 versus 460 min; P = 0.003) and a shorter cumulative length of hospital stay (23 versus 43 d; P = 0.002). Perioperative mortality (P = 0.257) did not differ significantly; however, patients with simultaneous resections had higher rates of grade 2 complications according to Clavien-Dindo (P < 0.001). Tumor-specific 1-y survival was 85 ± 5% for simultaneous and 83 ± 5% for staged resection (P = 0.631). On multivariable analysis, pT4 (P = 0.038), pN3 (P = 0.003), and G3/4 (P = 0.041) of the primary tumor and postoperative complications (Clavien-Dindo 3/4/5, P = 0.003) were poor prognostic factors regarding tumor-specific survival.

CONCLUSIONS

This is one of the largest and most thoroughly documented retrospective single-center studies of consecutive patients with synchronous hepatic metastases. Simultaneous resection of colorectal cancer together with hepatic metastases is a safe procedure in selected patients and does not have a significant influence on long-term survival.

Placement of Visually Impaired Persons: A Survey of Current Practices

Agencies offering vocational rehabilitation services for blind and visually impaired clients are involved in job placement using different models in terms of personnel and placement activities. In an effort to obtain information about personnel, types of activities, and other resources, agencies across the nation were surveyed. Using survey findings and available Rehabilitation Services Administration placement data, we noted that agencies employing both rehabilitation counselors and placement specialists were experiencing a higher rate of success than those agencies not employing placement specialists. We propose a model placement program employing both rehabilitation counselors and placement specialists, as well as rehabilitation technologists. Suggestions for model programs are made with an understanding of the pressures faced by the counselors and administrators: large caseloads, clients with multiple handicaps, and financial constraints.

Aging, Vision, and Work

Older people who lose their vision often do not return to competitive employment. Work, however, meets important, financial, psychological, and social needs. This article explores the variety of reasons why work is not always considered a rehabilitation alternative. Realistic factors that enhance competitive employment for this population are noted and information on available employment resources in the public and private sectors that will increase vocational opportunities is provided.

The Challenge of Upward Mobility

Many blind and visually impaired employees are working below their potential because of limited opportunity for upward mobility. This article explores the issues surrounding this problem, identifies existing resources, and includes the findings of the American Foundation for the Blind's Task Force on Upward Mobility which state the recommendations for rehabilitation and educational professionals, employers, and consumers.

Soft windowing application to improve analysis of high-throughput phenotyping data

Motivation

High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors.

Results

Here we introduce ‘soft windowing’, a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype–phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources.

Availability and implementation

The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin.

Supplementary information

Supplementary data are available at Bioinformatics online.

High Pressure Liquid Chromatographic Method for Indole in Shrimp: Development of Method and Collaborative Study

A collaborative study on the determination of indole in shrimp was conducted in which a high pressure liquid chromatographic (HPLC) method and a spectrofluorometric method were compared with the AOAC gas-liquid chromatographic (GLC) method (18.075–18.078,13th ed.). In the HPLC method, 10 g shrimp was blended with methanol, an internal standard was added, and the extract was filtered. Indole was separated on an octadecylsilane reverse phase column, using 60% MeOH-H2O, and quantitated with a fluorescence detector (excitation 280 nm, emission 330 nm) by comparing the indole peak height with that of an internal standard, 2-methylindole. Recoveries at a 25 μg/100 g level averaged 104% with a range of 90–127%, and at a level of 35 μg/100 g averaged 102% with a range of 93–112%. In the spectrofluorometric method, 25 g shrimp was extracted with 2% EtOAc-hexane. After several washes, indole was partitioned into a saturated NaCl-MeOH solution and its fluorescence was measured (excitation 280 nm, emission 332 nm). Recoveries at a 25 μg/100 g level averaged 93% with a range of 0–255% and at a level of 35 μg/100 g averaged 64% with a range of 0–107%. Recoveries obtained by the AOAC-GLC method at a level of 25 μg/100 g averaged 96% with a range of 81–116% and at a level of 35 μg/100 g averaged 101% with a range of 81–119%. The coefficients of variation were 20,10, and 64% at a 25 μg/100 g level for the GLC method, the HPLC method, and the spectrofluorometric method, respectively. The HPLC method was adopted as official first action for indole levels in shrimp exceeding 1 μg/100 g.

A 100-Year Review: A century of dairy processing advancements-Pasteurization, cleaning and sanitation, and sanitary equipment design

Over the past century, advancements within the mainstream dairy foods processing industry have acted in complement with other dairy-affiliated industries to produce a human food that has few rivals with regard to safety, nutrition, and sustainability. These advancements, such as milk pasteurization, may appear commonplace in the context of a modern dairy processing plant, but some consideration of how these advancements came into being serve as a basis for considering what advancements will come to bear on the next century of processing advancements. In the year 1917, depending on where one resided, most milk was presented to the consumer through privately owned dairy animals, small local or regional dairy farms, or small urban commercial dairies with minimal, or at best nascent, processing capabilities. In 1917, much of the retail milk in the United States was packaged and sold in returnable quart-sized clear glass bottles fitted with caps of various design and composition. Some reports suggest that the cost of that quart of milk was approximately 9 cents-an estimated $2.00 in 2017 US dollars. Comparing that 1917 quart of milk to a quart of milk in 2017 suggests several differences in microbiological, compositional, and nutritional value as well as flavor characteristics. Although a more comprehensive timeline of significant processing advancements is noted in the AppendixTable A1 to this paper, we have selected 3 advancements to highlight; namely, the development of milk pasteurization, cleaning and sanitizing technologies, and sanitary specifications for processing equipment. Finally, we provide some insights into the future of milk processing and suggest areas where technological advancements may need continued or strengthened attention and development as a means of securing milk as a food of high safety and value for the next century to come.

Garlic diallyl disulfide and diallyl trisulfide mitigates effects of pro-oxidant induced cellular stress and has immune modulatory function in LPS-stimulated porcine epithelial cells

The objective of the current study was to determine if garlic-derived diallyl disulfide (DADS) and diallyl trisulfide (DATS) could mitigate oxidative and endotoxin stress, using an intestinal porcine epithelial cell (IPEC-J2) model. The experiment was arranged as a 2 × 2 × 2 factorial of DADS + DATS (0 or 18 µM), pro-oxidant stressor (hydrogen peroxide at 0 or 100 µM), and endotoxin stressor (lipopolysaccharide [LPS] at 0 or 10 µg/mL) with 8 replicates per treatment. Cells were incubated with DADS + DATS for 18 h, LPS for 6 h, then with hydrogen peroxide for 3 h. Gene expression was measured by RT-PCR for cytokines, interleukin 8 (IL-8) and tumor necrosis factor α (TNF-α), and tight junction proteins, claudin 1 (CL-1), occludin (OC), and zonula occludens 1 (ZO-1). Trans-epithelial electrical resistance (TEER), the antioxidant enzyme catalase, and apical secretion of IL-8 protein into the incubation medium was also measured. There was an increase ( < 0.01) in TNF-α and IL-8 gene expression due to LPS, although there was no effect of hydrogen peroxide or DADS + DATS. Furthermore, there was a tendency for an increase ( = 0.08) in ZO-1 gene expression due to DADS + DATS. Treatment with DADS + DATS and hydrogen peroxide did not affect TEER, although there was a decrease ( = 0.02) in TEER with LPS incubation. Treatment of cells with hydrogen peroxide reduced catalase activity ( < 0.01), which was restored with pre-incubation of DADS + DATS ( < 0.10). There was an increase ( < 0.01) in IL-8 secretion due to LPS, which was further augmented ( < 0.01) by pre-incubation with DADS + DATS. Based on the results from the current study, DADS + DATS can ameliorate oxidative effects of hydrogen peroxide, as well as alter IL-8 secretion in LPS-treated IPEC-J2 cells.

Ability of garlic-derived diallyl disulfide and diallyl trisulfide supplemented by oral gavage to mitigate effects of an acute postweaning feed and water deprivation event in nursery pigs

Compounds in garlic have been shown to contain anti-inflammatory, antioxidant, and immune modulatory properties that may be able to mitigate the effects of nursery pig stressors. The objective of the current experiment was to determine if oral gavage of garlic-derived diallyl disulfide (DADS) and diallyl trisulfide (DATS) could mitigate the effects of a 24-h postweaning feed + water deprivation event in nursery pigs. Pigs (6.0 ± 0.05 kg and 21 d old) were allotted to 4 treatments in a randomized complete block design at weaning with 8 replicate pens per treatment that consisted of with or without a 24-h postweaning feed + water deprivation event and with or without an oral gavage containing 3.6 mg DADS + DATS/kg BW. Growth performance and morbidity were recorded throughout the experiment, and on 1, 6, and 21 d after weaning, 1 pig per pen was selected, blood was collected, the pig was euthanized, and a segment of the distal ileum was subsequently excised for morphological and gene and protein expression measurements. Mucosal gene expression was conducted by reverse transcription PCR for immune, antioxidant, and cellular integrity markers. Furthermore, activity of mucosal superoxide dismutase was measured by colorimetric assay. Immediately following the feed + water deprivation event, there was a decrease ( < 0.01) in growth performance and an increase ( = 0.01) in serum cortisol. The feed + water deprivation event tended ( = 0.10) to decrease ileal villus height and supplementation of DADS + DATS by oral gavage increased ( = 0.03) villus height 1 d after weaning. Supplementation of DADS + DATS by oral gavage decreased ( = 0.03) and tended to decrease ( = 0.08) gene expression of on 6 and 21 d after weaning, respectively. Furthermore, at 1 d after weaning, ileal mucosa SOD activity was decreased ( = 0.01) by the feed + water deprivation and increased ( = 0.04) by oral supplementation of DADS + DATS. Expression of the tight junction genes and were reduced ( ≤ 0.05) due to the feed + water deprivation event 1 d after weaning. Results from the current study show that an acute feed + water deprivation event can impact growth performance, intestinal characteristics, and antioxidant status in nursery pigs, which can be partially mitigated by oral supplementation of garlic compounds DADS + DATS.

Hygienic Shortcomings of Frozen Dessert Freezing Equipment and Fate of Listeria monocytogenes on Ice Cream-Soiled Stainless Steel

Although frozen dairy desserts have a strong record of safety, recent outbreaks of foodborne disease linked to ice creams have brought new attention to this industry. There is concern that small-scale frozen dessert equipment may not comply with or be reviewed against published comprehensive design and construction sanitation specifications (National Sanitation Foundation or 3-A sanitary standards). Equipment sanitary design issues may result in reduced efficacy of cleaning and sanitation, thus increasing the likelihood of postprocess contamination with pathogenic bacteria. In this context, and given that Listeria monocytogenes outbreaks are of great concern for the frozen dessert industry, a complementary study was conducted to evaluate the fate of L. monocytogenes in ice cream mix on a stainless steel surface. Our results showed that L. monocytogenes survived for up to 6 weeks at room temperature and 9 weeks at 4°C in contaminated ice cream on a stainless steel surface. Furthermore, chlorine- and acid-based surface sanitizers had no detrimental effect on the L. monocytogenes when used at a concentration and contact time (1 min) recommended by the manufacturer; significant reduction in CFU required 5 to 20 min of contact time.