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Cancer remains one of the leading causes of death globally. New immunotherapies that harness the patient’s immune system to fight cancer show promise, but their development requires analyzing the diversity of immune cells called T-cells. T-cells have receptors that recognize and bind to cancer cells. Sequencing these T-cell receptors allows to provide insights into their immune response, but extracting useful information is challenging. In this study, we propose a new computational method, TCellR2Vec, to select key features from T-cell receptor sequences for classifying different cancer types. We extracted features like amino acid composition, charge, and diversity measures and combined them with other sequence embedding techniques. For our experiments, we used a dataset of over 50,000 T-cell receptor sequences from five cancer types, which showed that TCellR2Vec improved classification accuracy and efficiency over baseline methods. These results demonstrate TCellR2Vec’s ability to capture informative aspects of complex T-cell receptor sequences. By improving computational analysis of the immune response, TCellR2Vec could aid the development of personalized immunotherapies tailored to each patient’s T-cells. This has important implications for creating more effective cancer treatments based on the individual’s immune system.

Abstract Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for selection in these two populations using newly sequenced whole-genomes of 54 highlanders and 74 lowlanders. We identified two candidate SNPs under selection - one in highlanders, associated with red blood cell traits and another in lowlanders, which is associated with white blood cell count – both potentially influencing the heart rate of Papua New Guineans in opposite directions. We also observed four candidate driver SNPs that exhibit linkage disequilibrium with an introgressed haplotype, highlighting the need to explore the possibility of adaptive introgression within these populations. This study reveals that the signatures of positive selection in highlanders and lowlanders of Papua New Guinea align closely with the challenges they face, which are specific to their environments.

Abstract Background Generating rigorous evidence to inform care for rare diseases requires reliable, sustainable, and longitudinal measurement of priority outcomes. Having developed a core outcome set for pediatric medium-chain acyl-CoA dehydrogenase (MCAD) deficiency, we aimed to assess the feasibility of prospective measurement of these core outcomes during routine metabolic clinic visits. Methods We used existing cohort data abstracted from charts of 124 children diagnosed with MCAD deficiency who participated in a Canadian study which collected data from birth to a maximum of 11 years of age to investigate the frequency of clinic visits and quality of metabolic chart data for selected outcomes. We recorded all opportunities to collect outcomes from the medical chart as a function of visit rate to the metabolic clinic, by treatment centre and by child age. We applied a data quality framework to evaluate data based on completeness, conformance, and plausibility for four core MCAD outcomes: emergency department use, fasting time, metabolic decompensation, and death. Results The frequency of metabolic clinic visits decreased with increasing age, from a rate of 2.8 visits per child per year (95% confidence interval, 2.3–3.3) among infants 2 to 6 months, to 1.0 visit per child per year (95% confidence interval, 0.9–1.2) among those ≥ 5 years of age. Rates of emergency department visits followed anticipated trends by child age. Supplemental findings suggested that some emergency visits occur outside of the metabolic care treatment centre but are not captured. Recommended fasting times were updated relatively infrequently in patients’ metabolic charts. Episodes of metabolic decompensation were identifiable but required an operational definition based on acute manifestations most commonly recorded in the metabolic chart. Deaths occurred rarely in these patients and quality of mortality data was not evaluated. Conclusions Opportunities to record core outcomes at the metabolic clinic occur at least annually for children with MCAD deficiency. Methods to comprehensively capture emergency care received at outside institutions are needed. To reduce substantial heterogeneous recording of core outcome across treatment centres, improved documentation standards are required for recording of recommended fasting times and a consensus definition for metabolic decompensations needs to be developed and implemented.

Data visualization plays a crucial role in gaining insights from high-dimensional datasets. ISOMAP is a popular algorithm that maps high-dimensional data into a lower-dimensional space while preserving the underlying geometric structure. However, ISOMAP can be computationally expensive, especially for large datasets, due to the computation of the pairwise distances between data points. The motivation behind this study is to improve efficiency by leveraging an approximate method, which is based on random kitchen sinks (RKS). This approach provides a faster way to compute the kernel matrix. Using RKS significantly reduces the computational complexity of ISOMAP while still obtaining a meaningful low-dimensional representation of the data. We compare the performance of the approximate ISOMAP approach using RKS with the traditional t-SNE algorithm. The comparison involves computing the distance matrix using the original high-dimensional data and the low-dimensional data computed from both t-SNE and ISOMAP. The quality of the low-dimensional embeddings is measured using several metrics, including mean squared error (MSE), mean absolute error (MAE), and explained variance score (EVS). Additionally, the runtime of each algorithm is recorded to assess its computational efficiency. The comparison is conducted on a set of protein sequences, used in many bioinformatics tasks. We use three different embedding methods based on k-mers, minimizers, and position weight matrix (PWM) to capture various aspects of the underlying structure and the relationships between the protein sequences. By comparing different embeddings and by evaluating the effectiveness of the approximate ISOMAP approach using RKS and comparing it against t-SNE, we provide insights on the efficacy of our proposed approach. Our goal is to retain the quality of the low-dimensional embeddings while improving the computational performance.

Abstract A soil bacterium in the Serratia genus, carrying a 153 kb conjugative amber disease‐associated plasmid (pADAP), is commercially exploited for population control of the New Zealand endemic pest beetle Costelytra giveni (Coleoptera: Scarabaeidae). The main insecticidal elements are an anti‐feeding prophage and the Sep ABC toxin complex (Tc). Homologs of pADAP, encoding variant Tcs, convey different beetle disease phenotypes. To investigate the correlation between variable bioactivity and the Tc variant, 76 Serratia plasmids were sequenced, resulting in the identification of four additional tc variants. All Serratia tc variants were found to be colocated with a conserved type 1 sef fimbrial‐like operon, indicating a conserved sef‐tc genetic island not observed outside of the Serratia genus. The conserved co‐location of the fimbrial and tc genes suggests the fimbriae somehow contribute to the lifestyle of Tc‐producing cells. Expression of the sef operon in a fim‐null Escherichia coli strain revealed fimbriae presence while a constructed sef‐deficient mutant showed no reduction of virulence or host colonization. Although no detectable contribution of Sef to amber disease in C. giveni was observed, the Sef adhesin sequences clustered similarly to the Serratia species encoding it, suggesting Sef has a species‐specific function.

Patient-physician communication has the potential to improve outcomes and satisfaction through the shared decision-making process (SDM). This study aims to assess the relationship between perception of SDM and demographic, clinical, and patient-reported outcomes in patients undergoing Hallux Valgus (HV) correction. A prospective analysis of 306 patients scheduled for HV surgery was completed. The CollaboRATE score was used to measure SDM. Multivariable linear regression model was used to assess whether SDM scores were associated with preoperative characteristics or postoperative outcome scores. The mean CollaboRATE score was 2.9 (SD 0.9) and did not differ by age, socioeconomic status, or sex. Lower CollaboRATE scores were associated with more symptoms of depression, lower socioeconomic status, and lower general health scores (p-value

Category: Ankle Arthritis; Ankle Introduction/Purpose: Currently there are two major surgical options for the treatment of end-stage ankle arthritis (ESAA), namely total ankle arthroplasty (TAA) and ankle arthrodesis (AA). Many patients inquire about what shoes they can expect to wear after surgery. Shoes should fit to the patient’s feet, help shielding pathological joints, be comfortable, but also fashionable, as they are part of personal style and fashion. The impact ESAA surgery has on choice of shoes and consecutively on quality of life, has not been studied. Potentially maintenance of ankle range of motion and improved gait mechanics with TAA could also improve the ability to comfortably wear different styles of shoes. The purpose of this study is to evaluate the effects of either AA and TAA on shoe-wear. Methods: This study is a retrospective analysis of a cohort of ESAA patients surgically treated with AA or TAA from the COFAS (Canadian Orthopaedic Foot and Ankle Society) database. Patient’s shoe wear comfort was obtained from the Musculoskeletal Outcomes Data Evaluation and Management Scale questionnaire, completed pre-operatively and post-operatively two and five years following surgery. The relationship between ankle-related quality of life and shoe-wear comfort, adjusting for patient factors was evaluated. A linear regression model adjusted for age, gender, BMI, smoking status, presence of inflammatory arthritis and baseline score was calculated. Additionally, differences within each pre-operative COFAS grades were analyzed. Results: 104 patients after AA and 106 following TAR have been included. The mean pre-operative baseline score did not differ between the cohorts (39.36 for AA and 38.94 for TAA, respectively; p= 0.74). Comparing AA patients with TAA patient scores over a 5-year period, there was no difference in shoe-wear comfort after 2 years, but after 5 years scores significantly improved for TAA patients (p= 0.02). Subgroup analysis showed that COFAS 4 patients improved the most with significant changes already after 2 years (mean difference 5.4, p=0.05), which further improved after 5 years of follow-up (mean difference 10.7, p=0.001). Conclusion: This study is the first study to elucidate patient experience after ankle arthrodesis and total ankle arthroplasty with regards to their shoe-wear. Patients undergoing TAR have better shoe-wear scores by five years post-operatively than those undergoing AA. Especially patients with a COFAS 4 grade, which represents a patient population with adjacent joint arthritis, show significant improvement already 2 years after surgery. This data is useful when counselling patients preoperatively, and further provides support for TAA over AA after appropriate patient selection.

Category: Ankle Arthritis; Hindfoot Introduction/Purpose: Ankle arthrodesis (AA) has, for many years, been considered the gold standard procedure for the surgical treatment of end stage ankle arthritis. Non-union following AA surgery is a devastating complication which subsequently requires revision surgery. However, data on outcomes including patient reported outcome measures (PROMs) following revision ankle arthrodesis (RAA) after failed AA is lacking. The aim of this study is to assess the outcome of RAA for symptomatic non-union after AA including PROMs. Methods: Prospectively collected data from a multicenter database of ankle arthritis surgery was analyzed. Demographic data and PROMs including Ankle Osteoarthritis Scale (AOS) and Short Form-36 (SF-36) health survey were collected at regular intervals. Surgeries were performed by six fellowship-trained foot and ankle surgeons between January 2003 and July 2015. 336 primary AA cases were identified, of which 27 (8%) underwent revision for symptomatic AA non-union. Results: Mean follow-up of 27 AA non-union cases was 5.3 years (2-10). There were 16 (59%) males and 11 (41%) females, with a mean age of 62 years (44 - 81) and a mean BMI of 32 (26.5 – 45), respectively. At index AA, 12 (44%) cases were performed arthroscopically. Twenty-three (84%) AA non-union patients were actively smoking pre- and post-operatively, and 15 (56%) were diabetic. Overall union-rate following RAA was 85% (23/27). For RAA the pre-operative mean AOS score of 64.9 (38.8-81.5) improved to 49.1 (24.1-73) at latest follow-up. SF-36 PCS score improved from 27.2 (21.3 – 38.3) to 33.3 (19.1-54.2) and SF-36 MCS score improved from 41.2 (17.5-60.9) to 46.2 (29.3-65.9). Overall complication rate of RAA was 22%, with a re-operation rate of 15%. Conclusion: Revision ankle arthrodesis (RAA) for ankle fusion non-union resulted in a successful fusion of the ankle in 85% of patients with modest improvement in AOS and SF-36 scores. Indeed, even after successful RAA, patients report pain and disability levels comparable to that reported by primary AA patients pre-operatively. Additionally, complication and re-operation rates of RAA are high. This data emphasizes on the importance of achieving a primary fusion in AA. The presented patient reported outcomes may help the treating surgeon to counsel patients prior to RAA surgery to better set their expectations.

Category: Ankle Arthritis; Ankle Introduction/Purpose: End-stage ankle arthritis causes severe pain and disability. The most common treatment has been ankle arthrodesis (AA) with proven long-term results. However, total ankle arthroplasty (TAA) has become a viable option to preserve ankle joint motion, relieve pain and shield adjacent joints. And with the evolution of TAA prostheses over the past 2 decades, the use of TAA has been steadily increasing. Nevertheless, long term outcome data on the latest generation of TAA prostheses is scarce. The primary purpose of this study is to evaluate long-term PROMs after Infinity™ TAA and to compare the outcome to a patient cohort of ankle arthrodesis (AA) performed during the same time period. Methods: Patients with end-stage ankle arthritis who received surgical treatment with a primary Infinity TAA or AA performed between 2013-2015 were included in this study. All surgeries were performed by four fellowship trained foot and ankle surgeons. Patient reported outcomes (PROMs) comprising the AOS and SF-36 PCS score were prospectively collected for patients who were willing to enroll into the Canadian Orthopaedic Foot and Ankle Society (COFAS) database. PROM data was compared between the TAA and AA patient cohorts. Implant survivorship as well as revision and reoperation rates were also analyzed. Results: 33 patients/ankles underwent primary Infinity™ TAA and 59 patients/ankles underwent AA. Of these, 25 TAA and 46 AA were enrolled in the prospective database, 20 and 46 had PROMs available for follow-up, respectively. Mean TAA PROM follow- up was 6.8 years (3-9) and for AA 6.4 years (2-9). Mean TAA age at surgery was 67 years (54-85) and 58 years for AA (27-84). TAA total AOS score pre-operatively was 52.9, which improved significantly to 23.9. SF-36 PCS scores improved from 33.1 to 43.3. Pre- and post-operative PROMs were similar to the AA cohort. At clinical follow up of 8-10 years, TAA implant survival was 97% with one metal component exchange. Two TAA patients had two reoperations each. In the AA cohort, the reoperation rate was 10.8%. Conclusion: This is the first report on patient reported outcomes and implant survival at 8 or more years after primary Infinity™ TAA. PROMs remain significantly improved at long term follow-up and are comparable to a cohort of long-term AA patients. Revision rates were low with a single component revision in 33 patients resulting in an implant survivorship of 97%. Long-term outcome of the Infinity™ total ankle arthroplasty is promising.

Abstract On November 30, 2021, the US Food and Drug administration (FDA) and the Center for Research on Complex Generics (CRCG) hosted a virtual public workshop titled “Establishing the Suitability of Model‐Integrated Evidence (MIE) to Demonstrate Bioequivalence for Long‐Acting Injectable and Implantable (LAI) Drug Products.” This workshop brought relevant parties from the industry, academia, and the FDA in the field of modeling and simulation to explore, identify, and recommend best practices on utilizing MIE for bioequivalence (BE) assessment of LAI products. This report summerized presentations and panel discussions for topics including challenges and opportunities in development and assessment of generic LAI products, current status of utilizing MIE, recent research progress of utilizing MIE in generic LAI products, alternative designs for BE studies of LAI products, and model validation/verification strategies associated with different types of MIE approaches.

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has generated a renewed interest in the larger family of Coronaviridae, which causes a variety of different respiratory infections in a variety of different hosts. Understanding the mechanisms behind the ability of a family of viruses to spill over into different hosts is an ongoing study. In this work, we studied the relationship between specific amino acid sites and the solvent accessibility of the surface (or spike) protein of different Coronaviridae. Since host specificity hinges on the portion(s) of the protein that interfaces with the host cell membrane, there could be a relationship between information gain in specific amino acid sites and solvent accessibility. We found a connection between sites with high information gain and solvent accessibility within several major subgenera of Coronaviridae. Such a connection could be used to study other lesser-known families of viruses, which is desirable because information gain is much easier to compute when the number of sequences is large, as we show. Finally, we produced a visualization of the sequences within each major subgenus and discussed several regions of interest, as well as focused on some pairs of Coronaviridae hosts of interest.

Abstract The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome—millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional approaches to understanding the diversity, dynamics, and evolution of viruses, is nonetheless a rich resource for machine learning (ML) approaches as alternatives for extracting such important information from these data. It is of hence utmost importance to design a framework for testing and benchmarking the robustness of these ML models. This paper makes the first effort (to our knowledge) to benchmark the robustness of ML models by simulating biological sequences with errors. In this paper, we introduce several ways to perturb SARS-CoV-2 genome sequences to mimic the error profiles of common sequencing platforms such as Illumina and PacBio. We show from experiments on a wide array of ML models that some simulation-based approaches with different perturbation budgets are more robust (and accurate) than others for specific embedding methods to certain noise simulations on the input sequences. Our benchmarking framework may assist researchers in properly assessing different ML models and help them understand the behavior of the SARS-CoV-2 virus or avoid possible future pandemics.

Summary: Borneo was a crossroad of ancient dispersals, with some of the earliest Southeast Asian human remains and rock art. The island is home to traditionally hunter-gatherer Punan communities, whose origins, whether of subsistence reversion or long-term foraging, are unclear. The connection between its past and present-day agriculturalist inhabitants, who currently speak Austronesian languages and have composite and complex genetic ancestry, is equally opaque. Here, we analyze the genetic ancestry of the northeastern Bornean Punan Batu (who still practice some mobile hunting and gathering), Tubu, and Aput. We find deep ancestry connections, with a shared Asian signal outgrouping modern and ancient Austronesian-ancestry proxies, suggesting a time depth of more than 7,500 years. They also largely lack the mainland Southeast Asian signals of agricultural Borneans, who are themselves genetically heterogeneous. Our results support long-term inhabitation of Borneo by some Punan ancestors and reveal unexpected complexity in the origins and dispersal of Austronesian-expansion-related ancestry.

Abstract The fungal genus Phytophthora includes an array of destructive plant pathogens that have had severe impacts on native, agricultural, and horticultural systems worldwide. Preventing the spread of Phytophthora species is critical for protecting vulnerable plants and ecosystems; yet detection remains a challenge due to their microscopic size, broad host range, and latent and cryptic expression in host plants. We tested the effectiveness of trained detection dogs to discriminate the odor of a target Phytophthora species, from among other non‐target odors, by conducting a multi‐choice experiment. We tasked two dogs with discriminating the scent of P. agathidicida—the causal agent of the lethal root rot disease “kauri dieback”—from two non‐target Phytophthora scents (P. cinnamomi and P. multivora), and four non‐target control treatments. We assessed the dogs' scent detection abilities by measuring the sensitivity and precision of their indications toward the target scent over 120 randomized trials. The dogs had a combined sensitivity of 68.6% (CI: 64.1–72.9) and precision of 52.2% (CI: 48.1–56.4), meaning they often identified P. agathidicida when it was present but also signaled on the other non‐target Phytophthora species. Moreover, we characterized the nature of false positive indications made for non‐target scents, which has important implications for how future multi‐choice experiments should be conducted. Our study shows that detection dogs are likely to be an adequate first‐pass detection tool for Phytophthora within a wider biosecurity framework. However, further research is warranted before dogs can be deployed for this purpose in the field.

Human existence is complemented by environmental sounds as by-products of people’s activities as well as intentionally generated sounds that allow human society to function, including transport and traffic sounds and notification sounds. The resulting soundscapes surround and permeate people’s daily existence. Technological, as well as behavioural change causes some of these sounds to become extinct at the local or universal level. While expressions of human communication through spoken words (language) and song are deemed to be heritage and thus formally collected and documented, there is a general lack of consideration of the heritage potential of anthropogenic environmental sounds. Focussing on examples from the state of NSW (Australia), this paper discusses sound loss in the urban heritage environment and advances two variations of a conceptual framework to assist heritage practitioners in decision-making to assess heritage potential in order to safeguard some of these sounds for the future.

Abstract Background Scab, caused by the biotrophic fungus Venturia inaequalis, is the most economically important disease of apples worldwide. During infection, V. inaequalis occupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many of these effectors are expected to be non-enzymatic proteins, some of which can be recognized by corresponding host resistance proteins to activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding of the roles that these effector proteins play in promoting subcuticular growth by V. inaequalis, as well as in activating, suppressing, or circumventing resistance protein-mediated defences in apple, is required. Results We generated the first comprehensive RNA-seq transcriptome of V. inaequalis during colonization of apple. Analysis of this transcriptome revealed five temporal waves of gene expression that peaked during early, mid, or mid-late infection. While the number of genes encoding secreted, non-enzymatic proteinaceous effector candidates (ECs) varied in each wave, most belonged to waves that peaked in expression during mid-late infection. Spectral clustering based on sequence similarity determined that the majority of ECs belonged to expanded protein families. To gain insights into function, the tertiary structures of ECs were predicted using AlphaFold2. Strikingly, despite an absence of sequence similarity, many ECs were predicted to have structural similarity to avirulence proteins from other plant-pathogenic fungi, including members of the MAX, LARS, ToxA and FOLD effector families. In addition, several other ECs, including an EC family with sequence similarity to the AvrLm6 avirulence effector from Leptosphaeria maculans, were predicted to adopt a KP6-like fold. Thus, proteins with a KP6-like fold represent another structural family of effectors shared among plant-pathogenic fungi. Conclusions Our study reveals the transcriptomic profile underpinning subcuticular growth by V. inaequalis and provides an enriched list of ECs that can be investigated for roles in virulence and avirulence. Furthermore, our study supports the idea that numerous sequence-unrelated effectors across plant-pathogenic fungi share common structural folds. In doing so, our study gives weight to the hypothesis that many fungal effectors evolved from ancestral genes through duplication, followed by sequence diversification, to produce sequence-unrelated but structurally similar proteins.

Despite church bell ringing being directly influenced by purposive human action, often as a liturgical function, it creates a community soundscape with ascribed heritage values. While general heritage management processes and decisions are informed by heritage professionals with a broader range of experience, we find that church bell ringing is contrary to this process. The COVID-19 pandemic has demonstrated how a stochastic disruptive event can dramatically alter soundscapes on a community-wide scale. Here, the effective power over bell ringing often rested with the individual clergy at the local level and is subject to that individual’s personal preferences. This has serious implications to non-traditional forms of heritage, such as intangible sounds and soundscapes. In realizing the value of sound signals and soundmarks, we highlight the need to formally recognize these sounds of religious settings and consider them in heritage frameworks.

Abstract Background Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom’s evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown. Results By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways. Conclusions The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi.

This paper examined the actual circumstances of the recent teacher shortage in public elementary and junior high schools in X Prefecture. Although teacher shortages had been reported, few previous studies had investigated them empirically. With the cooperation of all five branch offices of the Board of Education, data were collected through three surveys: 1) a questionnaire survey in June 2021 of the branch offices, 2) three interview surveys in July 2021 of the administrative officers at the town level, and 3) a 2019-2021 visiting survey of the branch offices of X Prefecture and of four towns. First, the actual amount of shortage as of May 1, 2021 was scrutinized by the questionnaire survey, clarifying the shortage into three stages. 1) Positions for 1,971 full-time teachers with tenure were unfilled as the first stage. 2) Teachers without tenure were subsequently recruited, still leaving 150 unfilled positions as the second stage. 3) Finally, part-time teachers were recruited, still leaving 115 unfilled positions as the third stage. 4) In the end, each school was required to manage by themselves. This survey also made it clear that the teacher shortage increased in each term because more and more teachers left work due to childbirth or illness, with no substitutes. This suggests that the design of the first national teacher shortage survey by the Ministry of Education in July 2021 should be redone, as it focused only on the condition of the first term. Second, the paper disclosed that the teacher shortage had increased since 2018 in this prefecture. This was caused by multiple factors at micro/mezzo/ macro levels at each stage. 1) There were three background factors for the first stage. (1) Although the numbers of teachers were strictly determined by national law, the government had made no improvements for 41 years. The local government had additionally decreased teacher numbers in order to prepare for a teacher surplus in the future, based on the declining birthrate. However, teacher demands were enlarged by the increase of children with special needs. (2) Administrators were reluctant to hire teachers with tenure. The risk of the prohibited surplus of teachers was multiplied because of the increased number of small and mutable special education classes. (3) The applicants for hiring exams decreased. Teaching itself was not as attractive as before. (4) Maternity leaves not only increased but grew longer. 2) The shortage in the second stage was caused by the lack of teachers without tenure. Few teachers were on the candidate list because most of them were already hired with tenure. 3) The shortage in the third stage was caused by the teacher license renewal system, which began in 2009. Many licenses were already expired. Third, the effects of the shortage were examined, finding that teachers were compelled to overwork because each school had to cover 3.91 teachers' worth of absence as a team. The paper also found that 60% of current teachers had less than 10 years' experience, which is expected to have negative effects both on the quality of teaching and the professionalization of teaching.

In the history of Japanese education, the "gender characteristics theory" that men and women naturally have different characteristics rejected not only the "gender equality theory" which came from Western Europe in the early Meiji era, but also the traditional "male chauvinism" of East Asia. According to the theory of gender characteristics, men and women were seen as having "equal value," though not "equal rights." This theory became the main educational philosophy of women's education when the single-sex school system was established in the 1900s, and likewise permeated society as a scientific theory in the 1920s. After World War II, when gender equality became accepted, a coeducational system was introduced toward equal educational opportunities. However, the gender characteristics theory remained the basis for making home economics a compulsory subject for women, as the division of labor by gender expanded during the high economic growth period of the sixties and environs. Coeducation was a system intended for men and women to "respect" each other and "cooperate" (Article 5 of the Basic Act on Education), and gender differences in curricula in coeducational schools were seen as "reasonable" differences to ensure "essential equality" between men and women. Schools were also not considered places of gender inequality. Elsewhere, women's universities and women's junior colleges were established after the war with the expectation that they would play a new role in training women to support the democratic society. However, they also inherited the pre-war vocational school curriculum centered on literature and home economics. When these colleges increased during the period of high economic growth, this prewar curriculum spread further, based on the gender characteristics theory. As a result, women's universities and women's junior colleges were criticized as contrary to gender equality. It was only after the 1985 ratification of the Convention on the Elimination of All Forms of Discrimination against Women and the spread of gender equality that the gender characteristics theory was finally rejected. Today, the raison d'être of girls' education is being questioned again. The Convention on the Elimination of All Forms of Discrimination Against Women not only rejects the gender characteristics theory and fixed gender roles, but also defines "discrimination against women" as "discrimination, exclusion or restriction based on sex." As the concept of gender spreads, the view that separating men and women is itself "discrimination" is also spreading. If women's education is to continue to exist, its raison d'être will depend on its ability to contribute to the elimination of gender disparities.

Required undergraduate diversity courses often expose students to topics and worldviews which may push them out of their comfort zones and prompt dissonance and even resistance. This paper reports on interviews with 68 faculty members across 16 humanities and social science disciplines at five predominantly white institutions in the Southern United States, detailing how they navigated discussion of controversial topics in required diversity courses. Most instructors aimed to expose students to critical social issues yet were concerned that resistance could disturb the learning process. We identified 20 unique strategies for handling controversial topics in class that included proactively establishing community and safety and normalizing conflict, and reactively acknowledging and surfacing multiple perspectives, as well as connecting content to students' lived experiences. Some instructors also reported a lack of controversy or conflict in their classrooms, which they variously attributed to student characteristics or their own disinclination to promote heated discussion - which, we argue, calls into question the breadth and criteria of many institutionally defined diversity course requirements. We conclude the paper with implications for faculty, educational developers, administrators, and institutions.

Abstract Here we describe a new, haploid and stroma forming species within the genus Epichloë, as Epichloë scottii sp. nov. The fungus was isolated from Melica uniflora growing in Bad Harzburg, Germany. Phylogenetic reconstruction using a combined dataset of the tubB and tefA genes strongly support that E. scottii is a distinct species and the so far unknown ancestor species of the hybrid E. disjuncta. A distribution analysis showed a high infection rate in close vicinity of the initial sampling site and only two more spots with low infection rates. Genetic variations in key genes required for alkaloid production suggested that E. scottii sp. nov. might not be capable of producing any of the major alkaloids including ergot alkaloid, loline, indole-diterpene and peramine. All isolates and individuals found in the distribution analysis were identified as mating-type B explaining the lack of mature stromata during this study. We further release a telomere-to-telomere de novo assembly of all seven chromosomes and the mitogenome of E. scottii sp. nov.

Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.

Summary: Kākāpō are a critically endangered species of parrots restricted to a few islands off the coast of New Zealand. Kākāpō are very closely monitored, especially during nesting seasons. In 2019, during a highly successful nesting season, an outbreak of aspergillosis affected 21 individuals and led to the deaths of 9, leaving a population of only 211 kākāpō. In monitoring this outbreak, cultures of aspergillus were grown, and genome sequenced. These sequences demonstrate that, very unusually for an aspergillus outbreak, a single strain of aspergillus caused the outbreak. This strain was found on two islands, but only one had an outbreak of aspergillosis; indicating that the strain was necessary, but not sufficient, to cause disease. Our analysis provides an understanding of the 2019 outbreak and provides potential ways to manage such events in the future.

Abstract Background An Informatics Consult has been proposed in which clinicians request novel evidence from large scale health data resources, tailored to the treatment of a specific patient. However, the availability of such consultations is lacking. We seek to provide an Informatics Consult for a situation where a treatment indication and contraindication coexist in the same patient, i.e., anti-coagulation use for stroke prevention in a patient with both atrial fibrillation (AF) and liver cirrhosis. Methods We examined four sources of evidence for the effect of warfarin on stroke risk or all-cause mortality from: (1) randomised controlled trials (RCTs), (2) meta-analysis of prior observational studies, (3) trial emulation (using population electronic health records (N = 3,854,710) and (4) genetic evidence (Mendelian randomisation). We developed prototype forms to request an Informatics Consult and return of results in electronic health record systems. Results We found 0 RCT reports and 0 trials recruiting for patients with AF and cirrhosis. We found broad concordance across the three new sources of evidence we generated. Meta-analysis of prior observational studies showed that warfarin use was associated with lower stroke risk (hazard ratio [HR] = 0.71, CI 0.39–1.29). In a target trial emulation, warfarin was associated with lower all-cause mortality (HR = 0.61, CI 0.49–0.76) and ischaemic stroke (HR = 0.27, CI 0.08–0.91). Mendelian randomisation served as a drug target validation where we found that lower levels of vitamin K1 (warfarin is a vitamin K1 antagonist) are associated with lower stroke risk. A pilot survey with an independent sample of 34 clinicians revealed that 85% of clinicians found information on prognosis useful and that 79% thought that they should have access to the Informatics Consult as a service within their healthcare systems. We identified candidate steps for automation to scale evidence generation and to accelerate the return of results. Conclusion We performed a proof-of-concept Informatics Consult for evidence generation, which may inform treatment decisions in situations where there is dearth of randomised trials. Patients are surprised to know that their clinicians are currently not able to learn in clinic from data on ‘patients like me’. We identify the key challenges in offering such an Informatics Consult as a service.

Annually, there are between 2500 and 3000 Christmas markets in Germany. While purported to be rooted in century-old tradition, the current concept of the markets, shaped in the 1930s, gradually transformed from primarily mercantile operations to experiential events. The experiential dimension is a collection of visual, auditory, and olfactory components that create a compound sensory response: the ‘Christmas atmosphere’. The prevalence of COVID-19 meant that traditional Christmas markets were largely absent from the festive calendar in Germany in 2020, disrupting the usual sensory experiences associated with these events. A review of the online presence showed that augmented markets and virtual reality were subsequently utilized in an attempt to re-create the experience and the ambience of the traditional markets, but had limited interactivity with many of the senses. We explore to what extent these multiple-sensory components may have been lost during the Christmas period of 2020 due to the COVID-19-induced transition from the traditional multisensory live market to a predominantly online experience, and highlight problems which arise through the documentation of such complex intangible heritage.