Lion Localizer: A software tool for inferring the provenance of lions (Panthera leo) using mitochondrial DNA

The illegal poaching of lions for their body parts poses a severe threat to lion populations across Africa. Poaching accounts for 35% of all human-caused lion deaths, with 51% attributed to retaliatory killings following livestock predation. In nearly half of the retaliatory killings, lion body parts are removed, suggesting that high demand for lion body parts may fuel killings attributed to human-lion conflict. Trafficked items are often confiscated in transit or destination countries far from their country of origin. DNA from lion parts may in some cases be the only available means for examining their geographic origins. In this paper, we present the Lion Localizer, a full-stack software tool that houses a comprehensive database of lion mitochondrial DNA (mtDNA) sequences sourced from previously published studies. The database covers 146 localities from across the African continent and India, providing information on the potential provenance of seized lion body parts. Lion mtDNA sequences of 350 or 1,140 bp corresponding to the cytochrome b region can be generated from lion products and queried against the Lion Localizer database. Using the query sequence, the Lion Localizer generates a listing of exact or partial matches, which are displayed on an interactive map of Africa. This allows for the rapid identification of potential regions and localities where lions have been or are presently being targeted by poachers. By examining the potential provenance of lion samples, the Lion Localizer serves as a valuable resource in the fight against lion poaching. The software is available at https://lionlocalizer.org.

The Impact of Variation in the Toll-like Receptor 3 Gene on Epizootic Hemorrhagic Disease in Illinois Wild White-Tailed Deer (Odocoileus virginianus)

Epizootic hemorrhagic disease (EHD) leads to high mortality in white-tailed deer (Odocoileus virginianus) and is caused by a double-stranded RNA (dsRNA) virus. Toll-like receptor 3 (TLR3) plays a role in host immune detection and response to dsRNA viruses. We, therefore, examined the role of genetic variation within the TLR3 gene in EHD among 84 Illinois wild white-tailed deer (26 EHD-positive deer and 58 EHD-negative controls). The entire coding region of the TLR3 gene was sequenced: 2715 base pairs encoding 904 amino acids. We identified 85 haplotypes with 77 single nucleotide polymorphisms (SNPs), of which 45 were synonymous mutations and 32 were non-synonymous. Two non-synonymous SNPs differed significantly in frequency between EHD-positive and EHD-negative deer. In the EHD-positive deer, phenylalanine was relatively less likely to be encoded at codon positions 59 and 116, whereas leucine and serine (respectively) were detected less frequently in EHD-negative deer. Both amino acid substitutions were predicted to impact protein structure or function. Understanding associations between TLR3 polymorphisms and EHD provides insights into the role of host genetics in outbreaks of EHD in deer, which may allow wildlife agencies to better understand the severity of outbreaks.

Fetal outcomes with and without the use of sugammadex in pregnant patients undergoing non-obstetric surgery: a multicenter retrospective study

BACKGROUND

The influence of sugammadex exposure during pregnancy on progesterone withdrawal and miscarriage is unknown. We aimed to compare the fetal outcomes in pregnant patients who had undergone non-obstetric surgery with and without sugammadex.

METHODS

We retrospectively reviewed the medical charts of pregnant women who underwent non-obstetric surgery at three tertiary perinatal care centers in Japan from January 2013 to December 2020. The women were divided into those who received general anesthesia with sugammadex (GA with SGX) and those who received general anesthesia without sugammadex (GA without SGX). We compared miscarriages and preterm births within four weeks after surgery.

RESULTS

Among the 124 women, 73 and 51 were included in the GA with SGX and GA without SGX groups, respectively. The two groups showed no differences in the rate of miscarriages or preterm births (3.0 % vs 4.3 %; odds ratio 1.42, 95 % confidence interval 0.19 to 10.47; P = 1.00). The SGX and no SGX groups were missing outcomes for 8.2 % and 7.8 % of cases, respectively.

CONCLUSIONS

Having GA with SGX or GA without SGX did not result in different rates of miscarriage or preterm birth within four weeks after the procedure. These findings do not exclude a potential association between sugammadex exposure during pregnancy and adverse pregnancy outcomes. Missing data may have obscured possible adverse outcomes from sugammadex exposure.

Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54-21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.

County-wide assessments of Illinois white-tailed deer (Odocoileus virginianus) prion protein gene variation using improved primers and potential implications for management

Chronic wasting disease (CWD) is a fatal, highly infectious prion disease that affects captive and wild cervids. Chronic wasting disease is the only known transmissible spongiform encephalopathy affecting free-ranging wildlife. In CWD-positive deer, some haplotypes of the prion protein gene PRNP are detected at lower frequencies as compared to CWD-negative deer, as are some variants of the prion protein PrP. Here, we examined wild, hunter-harvested CWD-negative white-tailed deer (Odocoileus virginianus) to determine whether there were geographical or temporal differences in the PRNP haplotypes, PRNP diplotypes, PrP proteoforms, and in the proportion of deer with at least one protective haplotype. We sampled 96-100 hunter-harvested deer per county at two time points in the Illinois counties of Jo Daviess, LaSalle, and Winnebago, chosen based on their geographic locations and known occurrence of CWD. The entire coding region of PRNP was sequenced, with haplotypes, diplotypes, and PrP proteoforms inferred. Across time, in Winnebago there was a significant increase in PrP proteoform F (p = 0.034), which is associated with a lower vulnerability to CWD. In every county, there was an increase over time in the frequency of deer carrying at least one protective haplotype to CWD, with a significant increase (p = 0.02) in the Jo Daviess County CWD infected region. We also found that primer combination was important as there was an 18.7% difference in the number of the deer identified as homozygous depending on primer usage. Current Illinois state management practices continue to remove CWD infected deer from locally infected areas helping to keep CWD prevalence low. Nonetheless, continued research on spatial and temporal changes in PRNP haplotypes, PrP proteoforms, and levels of deer vulnerability among Illinois deer will be important for the management of CWD within the state of Illinois and beyond.

Extrapolating the susceptibility of Eld’s deer (Rucervus eldii thamin) to chronic wasting disease from prion protein gene (PRNP) polymorphisms

Chronic wasting disease (CWD) is a prion disease of North American cervids. The transmission of CWD to endangered cervid species is of concern for captive breeding programs. Trans-species transmission could occur via direct contact with infected wild deer, or via prion contaminated fomites. Variation in the prion protein gene, PRNP, is associated with differences in CWD susceptibility among cervids. We therefore sequenced PRNP in 36 endangered Eld’s deer (Rucervus eldii thamin), detecting five synonymous and two non-synonymous SNPs. Three haplotypes were inferred, suggesting that genetic management in captive breeding programs has been effective at maintaining PRNP diversity. The haplotypes encoded two PrP protein variants. The more common Eld’s deer PrP variant encodes methionine at codon 208 and glutamine at codon 226. Because this protein variant is identical to a common PrP variant in white-tailed deer and mule deer and is especially common in white-tailed deer positive for CWD, we recommend reducing the frequency of this variant in the breeding stock, while implementing strict management practices to avoid exposure to wild North American cervids. The frequency of the other PrP variant, which differs from variants present in these North American cervids, was low. It has the potential to reduce susceptibility to CWD and thus could be increased in frequency. While PRNP haplotype frequencies should be shifted, genetic diversity should be maintained. Ultimately protein diversity may be protective should CWD infect the species, and trans-species polymorphisms are suggestive of past balancing selection and a potential fitness advantage for PRNP diversity.

Perspectives on follow-up care and research for childhood cancer survivors: results from an international SIOP meet-the-expert questionnaire in Kyoto, 2018

INTRODUCTION

Survival of childhood cancer has increased over the past decades. This has led to the development of strategies aiming to enhance follow-up care and research, for which priorities may vary globally. We explored perspectives of an international healthcare workers panel.

METHODS

Attendants of a meet-the-expert session on childhood cancer survivorship at the 2018 SIOP conference completed a survey about their view on important follow-up care and research aspects for survivors below and over 18 years. We analysed overarching categories and subtopics, and compared Asian versus European and North American healthcare workers.

RESULTS

A total of 58 participants from different medical specialties (67.2% paediatric oncologists) and continents (48.3% Asia, 39.7% Europe/North America) responded. Follow-up care priorities for survivors below and over 18 years included physical care (39.3% ≤18 years, 35.9% >18 years) and healthcare structure (29.4%, 26.0%). Physical care was also the most important research aspect for both age groups (52.5%, 50.7%). Psychological support was the most frequently reported subtopic. Asian clinicians (n = 22) primarily prioritized physical care aspects of follow-up care, whereas European/North American (n = 19) clinicians underscored the importance of healthcare structure.

CONCLUSION

Physical care is the most important aspect of survivorship care and research according to clinicians from several continents. Asian and European/North American respondents shared most priorities, however, healthcare structure was a more important category for European/North American clinicians. The most common subtopic was psychological support, underlining also the need to involve psychologists in follow-up.

Association of chronic wasting disease susceptibility with prion protein variation in white-tailed deer (Odocoileus virginianus)

Chronic wasting disease (CWD) is caused by prions, infectious proteinaceous particles, PrP^CWD. We sequenced the PRNP gene of 2,899 white-tailed deer (WTD) from Illinois and southern Wisconsin, finding 38 haplotypes. Haplotypes A, B, D, E, G and 10 others encoded Q₉₅G₉₆S₁₀₀N₁₀₃A₁₂₃Q₂₂₆, designated ‘PrP variant A.’ Haplotype C and five other haplotypes encoded PrP ‘variant C’ (Q₉₅S₉₆S₁₀₀N₁₀₃A₁₂₃Q₂₂₆). Haplotype F and three other haplotypes encoded PrP ‘variant F’ (H₉₅G₉₆S₁₀₀N₁₀₃A₁₂₃Q₂₂₆). The association of CWD with encoded PrP variants was examined in 2,537 tested WTD from counties with CWD. Relative to PrP variant A, CWD susceptibility was lower in deer with PrP variant C (OR = 0.26, p < 0.001), and even lower in deer with PrP variant F (OR = 0.10, p < 0.0001). Susceptibility to CWD was highest in deer with both chromosomes encoding PrP variant A, lower with one copy encoding PrP variant A (OR = 0.25, p < 0.0001) and lowest in deer without PrP variant A (OR = 0.07, p < 0.0001). There appeared to be incomplete dominance for haplotypes encoding PrP variant C in reducing CWD susceptibility. Deer with both chromosomes encoding PrP variant F (FF) or one encoding PrP variant C and the other F (CF) were all CWD negative. Our results suggest that an increased population frequency of PrP variants C or F and a reduced frequency of PrP variant A may reduce the risk of CWD infection. Understanding the population and geographic distribution of PRNP polymorphisms may be a useful tool in CWD management.

Prion Protein Gene (PRNP) Sequences Suggest Differing Vulnerability to Chronic Wasting Disease for Florida Key Deer (Odocoileus virginianus clavium) and Columbian White-Tailed Deer (O. v. leucurus)

Chronic wasting disease (CWD) is a fatal, highly transmissible spongiform encephalopathy caused by an infectious prion protein. CWD is spreading across North American cervids. Studies of the prion protein gene (PRNP) in white-tailed deer (WTD; Odocoileus virginianus) have identified non-synonymous substitutions associated with reduced CWD frequency. Because CWD is spreading rapidly geographically, it may impact cervids of conservation concern. Here, we examined the genetic vulnerability to CWD of 2 subspecies of WTD: the endangered Florida Key deer (O. v. clavium) and the threatened Columbian WTD (O. v. leucurus). In Key deer (n = 48), we identified 3 haplotypes formed by 5 polymorphisms, of which 2 were non-synonymous. The polymorphism c.574G>A, unique to Key deer (29 of 96 chromosomes), encodes a non-synonymous substitution from valine to isoleucine at codon 192. In 91 of 96 chromosomes, Key deer carried c.286G>A (G96S), previously associated with substantially reduced susceptibility to CWD. Key deer may be less genetically susceptible to CWD than many mainland WTD populations. In Columbian WTD (n = 13), 2 haplotypes separated by one synonymous substitution (c.438C>T) were identified. All of the Columbian WTD carried alleles that in other mainland populations are associated with relatively high susceptibility to CWD. While larger sampling is needed, future management plans should consider that Columbian WTD are likely to be genetically more vulnerable to CWD than many other WTD populations. Finally, we suggest that genetic vulnerability to CWD be assessed by sequencing PRNP across other endangered cervids, both wild and in captive breeding facilities.

[Nivolumab and Gamma Knife Radiosurgery for a Gastric Cancer Patient with Brain Metastasis-A Case Report]

The prognosis of patients with brain metastasis is very poor. Very few cases of combined treatment with nivolumab(240 mg/body, day 1, q2w, a programmed cell death-1[PD-1]inhibitor)and gamma knife radiosurgery(GKR)(27 Gy/3 Fr) for gastric cancer patients with brain metastasis have been reported. Here, we discuss the case of a 55-year-old man with HER2-positive poorly differentiated gastric adenocarcinoma with multiple bone and intra-abdominal lymph node metastases. After 25 courses of SOX(oxaliplatin 100 mg/m2, day 1, q3w plus S-1 120 mg/day, day 1-14, po, q3w)plus trastuzumab( 6 mg/kg, q3w)treatment, brain metastasis was detected. Subsequently, combined treatment with GKR and nivolumab(8 courses, anti-PD-1 monotherapy)was initiated. Both intra-abdominal and brain lesions decreased in response to this treatment, showing that combined therapy with nivolumab and GKR could be effective for treating gastric cancer patients with brain metastasis.

Impact of age on catheter ablation of premature ventricular contractions

Funding Acknowledgements

Type of funding sources: None.

Introduction

Catheter ablation (CA) of frequent premature ventricular contractions (PVC) is increasingly performed in older patients as the population ages.

Purpose

The purpose of this study was to assess the impact of age on procedural characteristics, safety and efficacy on PVC ablations.

Methods

Consecutive patients with symptomatic PVCs undergoing CA between 2015 and 2020 were evaluated. Acute ablation success was defined as the elimination of PVCs at the end of the procedure. Sustained success was defined as an elimination of symptoms, and  ≥80% reduction of PVC burden determined by Holter-ECG during long-term follow. Patients were sub-grouped based on age (&lt; 65 years vs. ≥ 65 years).

Results

A total of 114 patients were enrolled (median age 64 years, 71% males) and followed up for a median duration of 228 days. Baseline and procedural data were similar in both age groups. A left-sided origin of PVCs was more frequently observed in the elderly patient group compared to younger patients (83% vs. 67%, p = 0.04, Figure 1). The median procedure time was significantly shorter in elderly patients (160 min vs. 193 min, p = 0.02). The rates of both acute (86% vs. 92%, p = 0.32) and sustained success (70% vs. 71%, p = 0.90) were similar between groups. Complications rates (3.7%) did not differ between the two groups.

Conclusion

In a large series of patients with a variety of underlying arrhythmia substrates, similar rates of acute procedural success, complications, and ventricular arrhythmia-free-survival were observed after CA of PVCs. Older age alone should not be a reason to withhold CA of PVCs. Abstract Figure 1

A compact and stable incidence-plane-rotating second harmonics detector

We describe a compact and stable setup for detecting the optical second harmonics, in which the incident plane rotates with respect to the sample. The setup is composed of rotating Fresnel rhomb optics and a femtosecond ytterbium-doped fiber laser source operating at the repetition frequency of 10 MHz. The setup including the laser source occupies an area of 1 m² and is stable so that the intensity fluctuation of the laser harmonics can be less than 0.2% for 4 h. We present the isotropic harmonic signal of a gold mirror of 0.5 pW and demonstrate the integrity and sensitivity of the setup. We also show the polarization-dependent six-fold pattern of the harmonics of a few-layer WSe₂, from which we infer the degree of local-field effects. Finally, we describe the extensibility of the setup to investigate the samples in various conditions such as cryogenic, strained, ultrafast non-equilibrium, and high magnetic fields.

Characterization of 29 polymorphic microsatellite markers developed by genomic screening of Sumatran rhinoceros (Dicerorhinus sumatrensis)

Objective

The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling.

Results

Due to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; H_O = 0.30). These were sufficient to distinguish among individuals (P_ID < 0.0001), and to distinguish among siblings (P_ID(sib) < 0.0001). Among rhinos in Indonesia, almost all markers were established as polymorphic and effective for genotyping DNA from fecal samples. Notably, the markers amplified and displayed microsatellite polymorphisms using DNA extracted from 11 fecal samples collected non-invasively from wild Sumatran rhinoceros. These microsatellite markers provide an important resource for a census and genetic studies of wild Sumatran rhinos.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05522-x.

The SARC-F Score on Admission Predicts Falls during Hospitalization in Older Adults

OBJECTIVES

Community-dwelling older adults with sarcopenia are likely to fall. However, few studies have investigated whether sarcopenia is associated with falls during hospitalization in older adults. The purpose of this study was to determine whether the SARC-F when used as a simple screening tool for sarcopenia at the time of admission, predicts in-hospital falls.

DESIGN

A retrospective, observational study.

SETTING

A 900-bed university hospital.

PARTICIPANTS

A total of 9,927 patients aged 65 years and older were hospitalized at the hospital between April 2019 and March 2020.

MEASUREMENTS

The SARC-F contains five items: strength, assistance in walking, rise from a chair, climb stairs, and falls were evaluated at hospital admission. To investigate the relationship between the SARC-F score and falls, a ROC curve analysis was performed. Multivariate analysis adjusted for fall-related confounding factors such as age, gender, ADL, and disease were performed.

RESULTS

Mean age: 75.9±6.7 years; male: 56.2% were analyzed, and 159 patients (1.6%) fell during hospitalization. SARC-F scores at admission were significantly higher in the fall group than in the control group (3 [1-6] points vs. 0 [¬0-2] point, p<0.001). Statistical association was observed between the SARC-F and in-hospital fall (area under the curve = 0.721 [0.678-0.764], p < 0.001). The cut-off value for the highest sensitivity and specificity of the SARC-F score for in-hospital falls was two (sensitivity = 0.679, specificity = 0.715). Among the subitem of the SARC-F, the hazard ratios for climbing stairs were significantly higher (HR = 1.52 [1.10-2.09], p = 0.011) and for a history of fall was significantly higher (HR = 1.41 [1.02-1.95], p = 0.036). A SARC-F score ≥ 2 had a significantly higher incidence of in-hospital falls compared to a SARC-F score <2 (3.7% vs. 0.7%, p < 0.001). Also, a SARC-F score ≥ 2 had a significantly higher hazard ratio for falls (2.11 [1.37-3.26], p < 0.001).

CONCLUSION

SARC-F can help predict falls among hospitalized older adults.

SARC-F Predicts Mortality Risk of Older Adults during Hospitalization

OBJECTIVES

To determine the association between SARC-F scores and the in-hospital mortality risk among older patients admitted to acute care hospitals.

DESIGN

Single-center retrospective study.

SETTING

A university hospital.

PARTICIPANTS

All consecutive patients aged older than 65 were admitted and discharged from the study hospital between July 2019 and September 2019.

MEASUREMENTS

Relevant patient data included age, sex, body mass index, nutritional status, fat-free mass, disease, activities of daily living (ADL), duration of hospital stay, SARC-F, and occurrence of death within 30 days of hospitalization. The diseases that caused hospitalization and comorbidities (Charlson Comorbidity Index; CCI) were obtained from medical records. The Eastern Cooperative Oncology Group-performance status (PS) was used to determine ADL, and the in-hospital mortality rate within 30 days of hospitalization as the outcome.

RESULTS

We analyzed 2,424 patients. The mean age was 75.9±6.9 and 55.5% were male. Fifty-three in-hospital mortalities occurred among the participants within the first 30 days of hospitalization. Patients who died in-hospital were older, had poorer nutritional status and severer PS scores, and more comorbidities than those who did not. A SARC-F score of ≥4 predicted a higher mortality risk within those 30 days with the following precision: sensitivity 0.792 and specificity 0.805. There were significantly more deaths in Kaplan-Meier curves regarding a score of SARC-F≥4 than a score of SARC-F<4 (p<0.001). Cox proportional hazard analysis was used to identify the clinical indicators most associated with in-hospital mortality. SARC-F≥4 (Hazard Ratio: HR 5.65, p<0.001), CCI scores (HR1.11, p=0.004), and infectious and parasitic diseases (HR3.13, p=0.031) were associated with in-hospital mortality. The SARC-F items with significant in-hospital mortality effects were assistance with walking (HR 2.55, p<0.001) and climbing stairs (HR 2.46, p=0.002).

CONCLUSION

The SARC-F questionnaire is a useful prognostic indicator for older adults because a SARC-F ≥4 score during admission to an acute care hospital predicts in-hospital mortality within 30 days of hospitalization.

Effects of dietary gamma-cyclodextrin on voluntary activity and muscle strength in mice

Gamma-cyclodextrin (γCD) is a cyclic oligosaccharide consisting of eight α-(1,4)-linked glucopyranose subunits, which is often used in the food and pharmaceutical industries. However, little is known regarding the metabolic activity of "empty" γCD per se. Therefore, in the present study young C57BL/6 male mice received a control diet (CON) or an experimental diet that was supplemented with 12.88% γCD exchanged against corn starch. After 6 weeks of treatment, the voluntary wheel running activity was monitored and the muscle strength of mice was measured by employing Kondziela's inverted screen test and forelimb grip strength assay. The γCD-treated mice covered a significantly larger distance per night (CON 8.6 km, γCD 12.4 km) and were significantly longer active (CON 340 min, γCD 437 min). Moreover, γCD-treated mice significantly performed better at the inverted screen test indicated by an enhanced Kondziela score (CON 3.10, γCD 4.63). These data suggest that dietary γCD leads to an increased endurance. We also found a slightly anti-glycemic effect of γCD during oral glucose tolerance test. However, our mice from the γCD group exhibited no difference in terms of GLUT2 protein level in ileum tissue nor increased muscle glycogen storage. Furthermore, γCD exhibited no DPP-4 inhibitory activity in vitro. By analysing candidate muscle genes and proteins related to endurance and muscle performance we did not observe any differences in terms of Sirt1, Pgc1α, Cpt1b, Mef2c, Myh1 and Myh2 gene expression levels as well as total oxidative phosphorylation (OXPHOS), mtTFA and GLUT4 protein expression levels in skeletal muscle in response to γCD. We could not fully establish the exact underlying molecular mechanisms of the fitness improvement by dietary γCD which warrants further investigations.

Radiation Dose-escalated Chemoradiotherapy Using Simultaneous Integrated Boost Intensity-Modulated Radiotherapy for Locally Advanced Unresectable Thoracic Oesophageal Squamous Cell Carcinoma: A Single-institution Phase I Study

AIMS

About 80% of cases of locally advanced unresectable thoracic oesophageal squamous cell carcinoma recur within the irradiation fields after chemoradiotherapy. Radiation dose escalation using advanced radiotherapy techniques is expected to improve clinical outcomes by reducing local and regional recurrence. The current study aimed to determine the recommended escalated radiation dose for these patients.

MATERIALS AND METHODS

Patients with locally advanced unresectable thoracic oesophageal squamous cell carcinoma with good performance status underwent chemoradiotherapy using simultaneous integrated boost intensity-modulated radiotherapy (SIB-IMRT) with elective nodal irradiation. SIB-IMRT was delivered in five fractions per week. The radiation dose to the unresectable gross tumour was escalated from 66 Gy to a planned maximum dose of 72 Gy in 3 Gy increments in a standard 3 + 3 design. The doses to the resectable component, superficial tumours and elective nodal regions were fixed as 60, 51 and 48 Gy, respectively. Cisplatin and 5-fluorouracil were concurrently administered. Dose-limiting toxicity (DLT) was defined as acute grade 3 oesophagitis, grade 2 pneumonitis, grade 2 cardiac toxicity and a failure to complete planned radiotherapy within 60 days. Locoregional control and overall survival were estimated using the Kaplan-Meier method. Nine patients were enrolled.

RESULTS

DLTs occurred in one of six and two of three patients at doses of 66 and 69 Gy, respectively. All DLTs were grade 3 oesophagitis. The recommended dose was determined as 66 Gy delivered in 30 fractions based on the predefined criteria. With a median follow-up period of 23 months, the 1-year locoregional control and overall survival rates were 67 (95% confidence interval = 19-90) and 78% (95% confidence interval = 36-94), respectively.

CONCLUSION

The recommended radiation dose in chemoradiotherapy using SIB-IMRT with elective nodal irradiation was 66 Gy delivered in 30 fractions.

SARC-F as a Screening Tool for Sarcopenia and Possible Sarcopenia Proposed by AWGS 2019 in Hospitalized Older Adults

OBJECT

The SARC-F questionnaire is a sarcopenia screening tool. However, the validity of the SARC-F score ≥4 (SARC-F≥4) for the evaluation of sarcopenia in the hospital setting has not been investigated. This study investigated the validity of SARC-F≥4 as a screening tool for sarcopenia among hospitalized older adults.

DESIGN

Cross-sectional retrospective study.

SETTING

A university hospital.

PARTICIPANTS

This study included older adult patients (age ≥65 years) who were hospitalized at, and subsequently discharged from, the hospital between April and September 2019 and underwent a nutritional assessment by the nutrition support team during their hospitalization.

MEASUREMENTS

SARC-F was recorded at the time of admission, and the criteria specified by the Asia Working Group for Sarcopenia in 2019 (AWGS 2019) were applied to diagnose sarcopenia and possible sarcopenia. Appendicular muscle mass was estimated through validated equations, and three different models were developed for sarcopenia diagnosis. The sensitivity, specificity, and positive/negative likelihood ratios were calculated to analyze the accuracy of the SARC-F≥4 for sarcopenia and possible sarcopenia. Receiver-operating characteristic analyses were conducted to calculate the area under the curve (AUC).

RESULTS

In total, 1,689 patients (mean age: 77.2±7.3 years; male: 54.4%) were analyzed, and 636 patients (37.7%) had SARC-F≥4. Patients with SARC-F≥4 had a statistically significant higher prevalence of AWGS 2019-defined sarcopenia than patients with SARC-F <4 in the models (65.4-78.9% vs 40.9-45.2%, p<0.001). The sensitivity, specificity, and positive/negative likelihood ratios of SARC-F≥4 for sarcopenia and possible sarcopenia were 49.1-51.3%, 73.9-81.2%, and 1.88-2.72/0.60-0.69 and 48.0%, 84.5%, and 3.11/0.62, respectively. The AUC for sarcopenia and possible sarcopenia were 0.644-0.695 and 0.708, respectively. The AUC of SARC-F for possible sarcopenia was equivalent to or larger than that for sarcopenia (DeLong test p=0.438, 0.088, and <0.001 vs the three models).

CONCLUSIONS

SARC-F≥4 is suitable as a screening tool for sarcopenia in hospitalized older adults. SARC-F assessment could facilitate the detection and exclusion of sarcopenia at hospitalization and may lead to early adoption of a therapeutic and preventive approach.

Loxodonta Localizer: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA

Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins of elephants due to female elephant philopatry. Here, we introduce the Loxodonta Localizer (LL; www.loxodontalocalizer.org), an interactive software tool that uses a database of mtDNA sequences compiled from previously published studies to provide information on the potential provenance of confiscated ivory. A 316 bp control region sequence, which can be readily generated from DNA extracted from ivory, is used as a query. The software generates a listing of haplotypes reported among 1917 African elephants in 24 range countries, sorted in order of similarity to the query sequence. The African locations from which haplotype sequences have been previously reported are shown on a map. We demonstrate examples of haplotypes reported from only a single locality or country, examine the utility of the program in identifying elephants from countries with varying degrees of sampling, and analyze batches of confiscated ivory. The LL allows for the source of confiscated ivory to be assessed within days, using widely available molecular methods that do not depend on a particular platform or laboratory. The program enables identification of potential regions or localities from which elephants are being poached, with capacity for rapid identification of populations newly or consistently targeted by poachers.

A novel surgical strategy for the resection of duodenal gastrointestinal stromal tumours located close to the duodenal ampulla: a case report

Although the optimal surgical procedure for the resection of duodenal gastrointestinal stromal tumours has not yet been characterised due to the low prevalence of these tumours and the anatomical complexity of the duodenopancreatic region, difficult surgical procedures such as pancreaticoduodenectomy are often proposed for stromal tumours located in the second portion of the duodenum. Our case report highlights a novel surgical strategy that can be implemented as an alternative to pancreaticoduodenectomy for such tumours close to the duodenal ampulla. A 70-year-old man incidentally diagnosed with a stromal tumour close to the duodenal ampulla in the second portion of the duodenum underwent local resection guided by an endoscopic nasobiliary drainage tube with primary closure. This tube was converted to a percutaneous trans-small intestinal biliary drainage tube during the procedure to prevent biliary leakage biliary stasis due to swelling of the duodenal ampulla. He also underwent a simple distal gastrectomy with Roux-en-Y reconstruction. This resulted in successful R0 resection. There were no procedure-related complications or post-surgery weight changes. Our simple novel surgical strategy may therefore be useful for avoiding pancreaticoduodenectomy and maintaining quality of life in patients with stromal tumours close to the duodenal ampulla.

Ultrafast nematic-orbital excitation in FeSe

The electronic nematic phase is an unconventional state of matter that spontaneously breaks the rotational symmetry of electrons. In iron-pnictides/chalcogenides and cuprates, the nematic ordering and fluctuations have been suggested to have as-yet-unconfirmed roles in superconductivity. However, most studies have been conducted in thermal equilibrium, where the dynamical property and excitation can be masked by the coupling with the lattice. Here we use femtosecond optical pulse to perturb the electronic nematic order in FeSe. Through time-, energy-, momentum- and orbital-resolved photo-emission spectroscopy, we detect the ultrafast dynamics of electronic nematicity. In the strong-excitation regime, through the observation of Fermi surface anisotropy, we find a quick disappearance of the nematicity followed by a heavily-damped oscillation. This short-life nematicity oscillation is seemingly related to the imbalance of Fe 3d_xz and d_yz orbitals. These phenomena show critical behavior as a function of pump fluence. Our real-time observations reveal the nature of the electronic nematic excitation instantly decoupled from the underlying lattice.

Several experiments have shown evidence for unusual nematic electronic behaviour in unconventional superconductors. Here the authors use pump-probe spectroscopy to observe out-of-equilibrium behaviour of coupled nematic-orbital excitations in iron selenide.

Burden of Premorbid Consumption of Texture Modified Diets in Daily Life on Nutritional Status and Outcomes of Hospitalization

OBJECTIVES

Due to the water-rich cooking process required to soften texture modified diets (TMDs), TMDs may have poorer nutrition. The aim of this study was to investigate the associations between daily premorbid TMD consumption and nutritional status at the time of hospitalization, and its burden on hospitalization outcomes.

DESIGN

Retrospective observational study.

SETTING

An academic hospital.

PARTICIPANTS

The cohort comprised 3,594 older adult patients aged ≥65 years admitted to the hospital.

MEASUREMENTS

Patients were interviewed on admission using a premorbid daily consumption meal form to determine whether the patient ate a TMD. Nutritional status was examined using nutritional screening tools (Mini-Nutritional Assessment Short Form [MNA-SF], Malnutrition Universal Screening Tool [MUST], Geriatric Nutritional Risk Index [GNRI]) and the European Society of Clinical Nutrition and Metabolism (ESPEN)-defined criteria of malnutrition at admission. Length of hospital stay (LOS) and in-hospital mortality were considered outcomes of hospitalization. Multivariate analyses were performed to detect associations between premorbid TMD consumption and nutritional status and outcomes.

RESULTS

The mean age of the subjects was 75.9±7.0 years, including 58% males. Overall, 110 (3.1%) patients consuming a premorbid TMD were identified. They were older (p<0.001), had poor nutritional status (lower MNA-SF score [p<0.001] and GNRI value [p<0.001], higher MUST score [p<0.001], and more prevalent ESPEN-defined malnutrition [61.8% vs. 14.0%, p<0.001] than did patients without a TMD. The mortality rate and LOS of patients with TMD was higher (7.3% vs. 2.9%, p=0.017) and longer (19 days vs. 8 days, p<0.001) than those without TMD. Multivariate analyses showed that TMD consumption was independently associated with poor nutritional status and prolonged LOS after adjusting confounders.

CONCLUSION

Daily consumption of a TMD during the premorbid period affects nutritional status at the time of hospitalization and outcomes. Further studies are necessary to investigate whether nutritional intervention can improve outcomes for people on a TMD.

Influence of the geographic distribution of prion protein gene sequence variation on patterns of chronic wasting disease spread in white-tailed deer (Odocoileus virginianus)

Managing and controlling the spread of diseases in wild animal populations is challenging, especially for social and mobile species. Effective management benefits from information about disease susceptibility, allowing limited resources to be focused on areas or populations with a higher risk of infection. Chronic wasting disease (CWD), a transmissible spongiform encephalopathy that affects cervids, was detected in Colorado in the late 1960s. CWD was detected in Illinois and Wisconsin in 2002 and has since spread through many counties. Specific nucleotide variations in the prion protein gene (PRNP) sequence have been associated with reduced susceptibility to CWD in white-tailed deer. Though genetic resistance is incomplete, the frequency of deer possessing these mutations in a population is an important factor in disease spread (i.e. herd immunity). In this study we sequenced 625 bp of the PRNP gene from a sampling of 2433 deer from Illinois and Wisconsin. In north-central Illinois where CWD was first detected, counties had a low frequency of protective haplotypes (frequency <0.20); whereas in northwestern Illinois counties, where CWD cases have only more recently been detected, the frequency of protective haplotypes (frequency >0.30) was much higher (p < 0.05). Protective haplotype frequencies varied significantly among infected and uninfected geographic areas. The frequency of protective PRNP haplotypes may contribute to population level susceptibility and may shape the way CWD has spread through Illinois. Analysis of PRNP haplotype distribution could be a useful tool to assess CWD risk and allocate resources to contain and reduce the spread of infection.

SurePath® LBC improves the diagnostic accuracy of intrahepatic and hilar cholangiocarcinoma

INTRODUCTION

The current study aimed to compare cytology using SurePath^® (SP)-LBC and biliary tissue histology (BTH) for the diagnosis of biliary disease.

METHODS

Between January 2014 and December 2016, 57 patients underwent endoscopic retrograde cholangiopancreatography for the diagnosis of biliary disease. Biliary cytological samples were processed using SP-LBC and subsequently BTH was performed. A final diagnosis was confirmed by surgery (23 malignant cases) and clinical follow-up (34 benign and malignant cases): 18 extrahepatic cholangiocarcinoma; 17 intrahepatic/hilar cholangiocarcinoma (intra/H-CC); eight other malignant disease; and 14 benign biliary disease. The diagnoses made using SP-LBC and BTH were classified into four categories: (1) benign; (2) indeterminate; (3) suspicious for malignancy/malignant; and (4) inadequate. In addition, diagnostic accuracy was compared between SP-LBC and BTH.

RESULTS

Although 23% (13/57) of BTH samples were classified as inadequate, all SP-LBC cases were classified as adequate. Among 43 malignant cases, 11 normal, four indeterminate and 28 suspicious for malignancy/malignant were found using SP-LBC (26%, 9% and 65%, respectively), in contrast to 10 inadequate, nine normal, 10 indeterminate and 14 suspicious for malignancy/malignant observed using BTH (23%, 21%, 23%, and 33%, respectively). The identification of malignant cells was strikingly different between SP-LBC and BTH. Furthermore, limited to intra/H-CC, accuracy was significantly higher using SP-LBC than using BTH (P < .001).

CONCLUSIONS

SP-LBC of the biliary tract is a useful and reliable method for diagnosing biliary malignant disease and has an advantage over BTH for detecting malignant cells and accurately diagnosing intra/H-CC.

Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species, the African forest elephant (Loxodonta cyclotis)

The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants (Loxodonta cyclotis) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal. By contrast, the nuclear (nu) DNA phylogeography of forest elephants in Central Africa has not been determined. We therefore examined the population structure of Central African forest elephants by genotyping 94 individuals from six localities at 21 microsatellite loci. Between forest elephants in western and eastern Congolian forests, there was only modest genetic differentiation, a pattern highly discordant with that of mtDNA. Nuclear genetic patterns are consistent with isolation by distance. Alternatively, male-mediated gene flow may have reduced the previous regional differentiation in Central Africa suggested by mtDNA patterns, which likely reflect forest fragmentation during the Pleistocene. In species like elephants, male-mediated gene flow erases the nuclear genetic signatures of past climate and habitat changes, but these continue to persist as patterns in mtDNA because females do not disperse. Conservation implications of these results are discussed.

Functions to map photoelectron distributions in a variety of setups in angle-resolved photoemission spectroscopy

The distribution of photoelectrons acquired in angle-resolved photoemission spectroscopy can be mapped onto the energy-momentum space of the Bloch electrons in the crystal. The explicit forms of the mapping function f depend on the configuration of the apparatus as well as on the type of the photoelectron analyzer. We show that the existence of the analytic forms of f^-1 is guaranteed in a variety of setups. The variety includes the case when the analyzer is equipped with a photoelectron deflector. Thereby, we provide a demonstrative mapping program implemented by an algorithm that utilizes both f and f^-1. The mapping methodology is also usable in other spectroscopic methods such as momentum-resolved electron-energy loss spectroscopy.

Evaluation of the Function of Primary Human Hepatocytes Co-Cultured with the Human Hepatic Stellate Cell (HSC) Line LI90

Most bioartificial liver devices utilise primary hepatocytes alone although some have considered the use of non parenchymal cells in addition. However the effects of co-culture of human hepatocytes with different sinusoidal cell types has not been fully investigated. In this study we have examined the influence of co-culturing primary human hepatocytes with the human hepatic stellate cell (HSC) line, LI90. Cultures were monitored by light microscopy and on days 4, 8 and 14 urea synthesis and cytochrome P450 activity were measured. Morphologically LI90 cells proliferated to fill spaces between and into adjacent islands of hepatocytes. On day 14 cytochrome P450 activity in co-culture was significantly improved compared to hepatocytes cultured alone. By contrast, urea synthesis in hepatocytes was unaffected by single or co-culture. Therefore it can be concluded that a combination of primary human hepatocytes with LI90 cells is beneficial for growth and some stability of hepatocytes and may therefore be appropriate for seeding bioartificial liver devices.

Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions

Viruses of the subfamily Orthoretrovirinae are defined by the ability to reverse transcribe an RNA genome into DNA that integrates into the host cell genome during the intracellular virus life cycle. Exogenous retroviruses (XRVs) are horizontally transmitted between host individuals, with disease outcome depending on interactions between the retrovirus and the host organism. When retroviruses infect germ line cells of the host, they may become endogenous retroviruses (ERVs), which are permanent elements in the host germ line that are subject to vertical transmission. These ERVs sometimes remain infectious and can themselves give rise to XRVs. This review integrates recent developments in the phylogenetic classification of retroviruses and the identification of retroviral receptors to elucidate the origins and evolution of XRVs and ERVs. We consider whether ERVs may recurrently pressure XRVs to shift receptor usage to sidestep ERV interference. We discuss how related retroviruses undergo alternative fates in different host lineages after endogenization, with koala retrovirus (KoRV) receiving notable interest as a recent invader of its host germ line. KoRV is heritable but also infectious, which provides insights into the early stages of germ line invasions as well as XRV generation from ERVs. The relationship of KoRV to primate and other retroviruses is placed in the context of host biogeography and the potential role of bats and rodents as vectors for interspecies viral transmission. Combining studies of extant XRVs and "fossil" endogenous retroviruses in koalas and other Australasian species has broadened our understanding of the evolution of retroviruses and host-retrovirus interactions.

Perceptions of dental students in Japanese national universities about studying abroad

PURPOSE

Dental faculties in Japan have organised many short-term international exchange programs to enable their undergraduates to study abroad. However, not many students apply for those programs. In this present study, we attempted to clarify the factors that discourage undergraduate dental students from studying abroad.

METHODS

We administered a questionnaire survey to 512 undergraduate dental students in three national universities located in different areas in Japan.

RESULTS

Although 61.7% of the participants expressed interest in studying abroad, only 19.1% of them had prior experiences of study abroad or plans to do so. Their main worries were about lack of sufficient language ability in academic fields. Comparing those who were interested in studying abroad with those who were not revealed significant differences regarding their concern about lack of language ability and lack of specialised knowledge in dentistry. Participants who did not want to study abroad indicated that they did not perceive a purpose in doing so and cited not having foreign friends as a problem. Household income was significantly correlated with concerns about overall expenses.

CONCLUSION

Overall, language ability and academic knowledge appeared to be the two strongest factors affecting dental students' consideration of studying abroad. Dental schools in Japan can use the findings of this study to improve their undergraduate exchange programs in such a way as to stimulate greater interest amongst their students.