Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Compositions and Their Seasonal Shifts in Japanese Resident Birds, Estimated from the Analysis of Volunteer Monitoring Data

Determining the composition of a bird’s diet and its seasonal shifts are fundamental for understanding the ecology and ecological functions of a species. Various methods have been used to estimate the dietary compositions of birds, which have their own advantages and disadvantages. In this study, we examined the possibility of using long-term volunteer monitoring data as the source of dietary information for 15 resident bird species in Kanagawa Prefecture, Japan. The data were collected from field observations reported by volunteers of regional naturalist groups. Based on these monitoring data, we calculated the monthly dietary composition of each bird species directly, and we also estimated unidentified items within the reported foraging episodes using Bayesian models that contained additional information regarding foraging locations. Next, to examine the validity of the estimated dietary compositions, we compared them with the dietary information for focal birds based on stomach analysis methods, collected from past literatures. The dietary trends estimated from the monitoring data were largely consistent with the general food habits determined from the previous studies of focal birds. Thus, the estimates based on the volunteer monitoring data successfully detected noticeable seasonal shifts in many of the birds from plant materials to animal diets during spring—summer. Comparisons with stomach analysis data supported the qualitative validity of the monitoring-based dietary information and the effectiveness of the Bayesian models for improving the estimates. This comparison suggests that one advantage of using monitoring data is its ability to detect dietary items such as fleshy fruits, flower nectar, and vertebrates. These results emphasize the potential importance of observation data collecting and mining by citizens, especially free descriptive observation data, for use in bird ecology studies.
Pertussis Post-Exposure Prophylaxis among Household Contacts: A Cost-Utility Analysis

Background Recent pertussis outbreaks have prompted re-examination of post-exposure prophylaxis (PEP) strategies, when immunization is not immediately protective. Chemoprophylaxis is recommended to household contacts; however there are concerns of clinical failure and significant adverse events, especially with erythromycin among infants who have the highest disease burden. Newer macrolides offer fewer side effects at higher drug costs. We sought to determine the cost-effectiveness of PEP strategies from the health care payer perspective. Methods A Markov model was constructed to examine 4 mutually exclusive strategies: erythromycin, azithromycin, clarithromycin, or no intervention, stratified by age group of contacts (“infant”, “child”, and “adult”). Transition probabilities, costs and quality-adjusted life years (QALYs) were derived from the literature. Chronic neurologic sequelae were modeled over a lifetime, with costs and QALYs discounted at 5%. Associated health outcomes and costs were compared, and incremental cost-effectiveness ratios (ICER) were calculated in 2012 Canadian dollars. Deterministic and probabilistic sensitivity analyses were performed to evaluate the degree of uncertainty in the results. Findings Azithromycin offered the highest QALYs in all scenarios. While this was the dominant strategy among infants, it produced an ICER of $16,963 per QALY among children and $2,415 per QALY among adults. Total QALYs with azithromycin were 19.7 for a 5-kg infant, 19.4 for a 10-year-old child, and 18.8 for a 30-year-old adult. The costs of azithromycin PEP among infants, children and adults were $1,976, $132 and $90, respectively. While results were sensitive to changes in PEP effectiveness (11% to 87%), disease transmission (variable among age groups) and hospitalization costs ($379 to $59,644), the choice of strategy remained unchanged. Interpretation Pertussis PEP is a cost-effective strategy compared with no intervention and plays an important role in contact management, potentially in outbreak situations. From a healthcare payer perspective, azithromycin is the optimal strategy among all contact groups.
Phosphoenolpyruvate Carboxykinase 1 Gene (Pck1) Displays Parallel Evolution between Old World and New World Fruit Bats

Bats are an ideal mammalian group for exploring adaptations to fasting due to their large variety of diets and because fasting is a regular part of their life cycle. Mammals fed on a carbohydrate-rich diet experience a rapid decrease in blood glucose levels during a fast, thus, the development of mechanisms to resist the consequences of regular fasts, experienced on a daily basis, must have been crucial in the evolution of frugivorous bats. Phosphoenolpyruvate carboxykinase 1 (PEPCK1, encoded by the Pck1 gene) is the rate-limiting enzyme in gluconeogenesis and is largely responsible for the maintenance of glucose homeostasis during fasting in fruit-eating bats. To test whether Pck1 has experienced adaptive evolution in frugivorous bats, we obtained Pck1 coding sequence from 20 species of bats, including five Old World fruit bats (OWFBs) (Pteropodidae) and two New World fruit bats (NWFBs) (Phyllostomidae). Our molecular evolutionary analyses of these sequences revealed that Pck1 was under purifying selection in both Old World and New World fruit bats with no evidence of positive selection detected in either ancestral branch leading to fruit bats. Interestingly, however, six specific amino acid substitutions were detected on the ancestral lineage of OWFBs. In addition, we found considerable evidence for parallel evolution, at the amino acid level, between the PEPCK1 sequences of Old World fruit bats and New World fruit bats. Test for parallel evolution showed that four parallel substitutions (Q276R, R503H, I558V and Q593R) were driven by natural selection. Our study provides evidence that Pck1 underwent parallel evolution between Old World and New World fruit bats, two lineages of mammals that feed on a carbohydrate-rich diet and experience regular periods of fasting as part of their life cycle.
Exploiting Structure in Backtracking Algorithms for Propositional and Probabilistic Reasoning

Boolean propositional satisfiability (SAT) and probabilistic reasoning represent two core problems in AI. Backtracking based algorithms have been applied in both problems. In this thesis, I investigate structure-based techniques for solving real world SAT and Bayesian networks, such as software testing and medical diagnosis instances. When solving a SAT instance using backtracking search, a sequence of decisions must be made as to which variable to branch on or instantiate next. Real world problems are often amenable to a divide-and-conquer strategy where the original instance is decomposed into independent sub-problems. Existing decomposition techniques are based on pre-processing the static structure of the original problem. I propose a dynamic decomposition method based on hypergraph separators. Integrating this dynamic separator decomposition into the variable ordering of a modern SAT solver leads to speedups on large real world SAT problems. Encoding a Bayesian network into a CNF formula and then performing weighted model counting is an effective method for exact probabilistic inference. I present two encodings for improving this approach with noisy-OR and noisy-MAX relations. In our experiments, our new encodings are more space efficient and can speed up the previous best approaches over two orders of magnitude. The ability to solve similar problems incrementally is critical for many probabilistic reasoning problems. My aim is to exploit the similarity of these instances by forwarding structural knowledge learned during the analysis of one instance to the next instance in the sequence. I propose dynamic model counting and extend the dynamic decomposition and caching technique to multiple runs on a series of problems with similar structure. This allows us to perform Bayesian inference incrementally as the evidence, parameter, and structure of the network change. Experimental results show that my approach yields significant improvements over previous model counting approaches on multiple challenging Bayesian network instances.
Significance of Oxygen Supply in Jarosite Biosynthesis Promoted by Acidithiobacillus ferrooxidans

Jarosite [(Na+, K+, NH4 +, H3O+)Fe3(SO4)2(OH)6] is an efficient scavenger for trace metals in Fe- and SO4 2--rich acidic water. During the biosynthesis of jarosite promoted by Acidithiobacillus ferrooxidans, the continuous supply of high oxygen levels is a common practice that results in high costs. To evaluate the function of oxygen in jarosite production by A. ferrooxidans, three groups of batch experiments with different oxygen supply levels (i.e., loading volume percentages of FeSO4 solution of 20%, 40%, and 70% v/v in the flasks), as well as three groups of sealed flask experiments with different limiting oxygen supply conditions (i.e., the solutions were not sealed at the initial stage of the ferrous oxidation reaction by paraffin but were rather sealed at the end of the ferrous oxidation reaction at 48 h), were tested. The formed Fe-precipitates were characterized via X-ray powder diffraction and scanning electron microscope-energy dispersive spectral analysis. The results showed that the biosynthesis of jarosite by A. ferrooxidans LX5 could be achieved at a wide range of solution loading volume percentages. The rate and efficiency of the jarosite biosynthesis were poorly correlated with the concentration of dissolved oxygen in the reaction solution. Similar jarosite precipitates, expressed as KFe3 (SO4) 2(OH)6 with Fe/S molar ratios between 1.61 and 1.68, were uniformly formed in unsealed and 48 h sealed flasks. These experimental results suggested that the supply of O2 was only essential in the period of the oxidation of ferrous iron to ferric but was not required in the period of ferric precipitation.
High Performance Thermal Grease with Aluminum Nitride Filler and an Installation for Thermal Conductivity Investigation

A huge increase in performance of devices within the sizes and weight decrease result in high performance thermal interface materials (TIM) are indispensable to application. Thermal grease is one of the most commonly used TIM types. Zinc-oxide based thermal grease (KPT-8) has a low thermal conductivity that leads to overheating. New silicone oil – aluminum nitride high performance thermal grease has been studied. Also the installation for thermal conductivity investigation has been designed and produced. Thermal conductivity value of aluminum nitride-silicone oil thermal grease with 50 % volume fraction was 1,130±0,056 W/(m K), that is 40 % higher than KPT-8 thermal conductivity. Thermal conductivity value was calculated by a number of theoretical models, and the results were compared to the experimental data. The best results have been obtained by modeling within Brugemman and Cheng-Vachon theories.
Cell-Free Propagation of Coxiella burnetii Does Not Affect Its Relative Virulence

Q fever is caused by the obligate intracellular bacterium Coxiella burnetii. In vitro growth of the bacterium is usually limited to viable eukaryotic host cells imposing experimental constraints for molecular studies, such as the identification and characterisation of major virulence factors. Studies of pathogenicity may benefit from the recent development of an extracellular growth medium for C. burnetii. However, it is crucial to investigate the consistency of the virulence phenotype of strains propagated by the two fundamentally different culturing systems. In the present study, we assessed the viability of C. burnetii and the lipopolysaccaride (LPS) encoding region of the bacteria in both culture systems as indirect but key parameters to the infection potential of C. burnetii. Propidium monoazide (PMA) treatment-based real-time PCR was used for enumeration of viable C. burnetii which were validated by fluorescent infectious focus forming unit counting assays. Furthermore, RNA isolated from C. burnetiipropagated in both the culture systems was examined for LPS-related gene expression. All thus far known LPS-related genes were found to be expressed in early passages in both culturing systems indicating the presence of predominantly the phase I form of C. burnetii. Finally, we used immune-competent mice to provide direct evidence, that the relative virulence of different C. burnetii strains is essentially the same for both axenic and cell-based methods of propagation.
A hybrid retention time alignment algorithm for SWATH‐MS data

Recently, data‐independent acquisition (DIA) MS has gained popularity as a qualitative–quantitative workflow for proteomics. One outstanding problem in the analysis of DIA‐MS data is alignment of chromatographic retention times across multiple samples, which facilitates peptide identification and accurate quantification. Here, we present a novel hybrid (profile‐based and feature‐based) algorithm for LC‐MS alignment and test it on sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) (a type of DIA) data. Our algorithm uses a profile‐based dynamic time warping algorithm to obtain a coarse alignment and corrects large retention time shifts, and then uses a feature‐based bipartite matching algorithm to match feature to feature at a fine scale. We evaluated our method by comparing our aligned feature pairs to peptide identification results of pseudo‐MS2 spectra exported by DIA‐Umpire, a recently reported tool for deconvoluting DIA‐MS data. We proposed that our method can be used to align DIA‐MS data prior to identification, and the alignment can be used to delete noise peaks or screen for differentially changed features. We found that a simple alignment‐enabled denoising scheme can reduce the number of pseudo‐MS2 spectra exported by DIA‐Umpire by up to around 40%, while retaining a comparable number of identifications. Finally, we demonstrated the utility of our tool for accurate label‐free relative quantification across multiple SWATH runs.
The Effect of Financial Compensation on Health Outcomes following Musculoskeletal Injury: Systematic Review

The effect of financial compensation on health outcomes following musculoskeletal injury requires further exploration because results to date are varied and controversial. This systematic review identifies compensation related factors associated with poorer health outcomes following musculoskeletal injury. Searches were conducted using electronic medical journal databases (Medline, CINAHL, Embase, Informit, Web of Science) for prospective studies published up to October 2012. Selection criteria included: prognostic factors associated with validated health outcomes; six or more months follow up; and multivariate statistical analysis. Studies solely measuring return to work outcomes were excluded. Twenty nine articles were synthesised and then assessed using GRADE (Grading of Recommendations Assessment, Development and Evaluation) methodology to determine evidence levels. The results were mixed. There was strong evidence of an association between compensation status and poorer psychological function; and legal representation and poorer physical function. There was moderate evidence of an association between compensation status and poorer physical function; and legal representation and poorer psychological function. There was limited evidence of an association between compensation status and increased pain. In seven studies the association depended on the outcome measured. No studies reported an association between compensation related factors and improved health outcomes. Further research is needed to find plausible reasons why compensation related factors are associated with poorer health following musculoskeletal injury.
Cajal bodies and snRNPs - friends with benefits

ABSTRACT Spliceosomal snRNPs are complex particles that proceed through a fascinating maturation pathway. Several steps of this pathway are closely linked to nuclear non-membrane structures called Cajal bodies. In this review, I summarize the last 20 y of research in this field. I primarily focus on snRNP biogenesis, specifically on the steps that involve Cajal bodies. I also evaluate the contribution of the Cajal body in snRNP quality control and discuss the role of snRNPs in Cajal body formation.
Genetic Investigation of Bisphosphonate-Related Osteonecrosis of Jaw (BRONJ) via Whole Exome Sequencing and Bioinformatics

Complications associated with the use of bisphosphonate (BP) have risen over the years due to an increase in the prescription of BP. BP-related osteonecrosis of jaw (BRONJ), one of the complications linked to the consumption of BP, greatly affects patients with minor dental trauma, incurring a long healing period. While BRONJ afflicts only a minority of patients prescribed with BP, BRONJ is a multigenic disease affected both by environmental and genetic factors having a distinctive phenotype. This study aims to discover genetic biomarkers associated with BRONJ via whole exome sequencing (WES) followed by statistical analysis. Sixteen individuals who had been prescribed with bisphosphonate medication and diagnosed as BRONJ were chosen and each individual’s saliva sample was collected for WES. 126 randomized subsamples from the GSK project representing 109 male and 17 female Koreans were used as a control data set. Fisher’s exact test was carried out to assess the significance of genetic variants in BRONJ patients. Gene set enrichment analysis (GSEA) (DAVID Bioinformatics Resource 6.7) was used to perform a cluster analysis of variants found from Fisher‘s exact test. The results from this study suggest that BRONJ-inducing factors are genetically associated and BRONJ occurs due to the malfunctioning of post-translational modification in osteoclast leading to the impairment of cell morphology and adhesion.
MOLECULAR DYNAMICS SIMULATION OF NANOSCALE WEAR IN ATOMIC FORCE MICROSCOPY

Wear is the loss or displacement of material due to contact or relative motion between bodies. Wear plays an important role in the performance of tribological components and is undesirable in most machine applications. Wear is also important for small scale instruments such as the atomic force microscope (AFM). The AFM has become one of the most widely used tools in the fields of nanoscience and nanotechnology for the preparation and analysis of surfaces and materials. It has been shown that AFM tip wear affects the performance and operating life of the AFM used for applications such as nanomanufacturing, nanoscale metrology and probe-based data storage applications. As AFM techniques advance from use in research laboratories to industrial applications, the durability and stability of the tip itself become more critical. However, the fundamental wear mechanisms and how wear affects the performance of precision components at the nanoscale are not fully understood. Thus, it is necessary to explore the qualitative as well as quantitative nature of nanoscale wear. In this thesis, we studied the mechanisms of nanoscale wear in contact mode AFM and explored the effect of tip wear on topography measurement in amplitude modulation AFM using molecular dynamics (MD) simulation. We characterized wear in terms of the structural and chemical evolution of the sliding surfaces, which revealed that nanoscale wear can occur through both adhesion and abrasion. Wear during running-in was also studied and it was observed that crystalline materials may become amorphous before they are removed from the surface. We then studied the effects of load, adhesive strength and surface roughness on nanoscale wear, and the results suggested that it is possible to identify optimum sliding conditions to minimize wear. In addition, we developed a model of amplitude modulation AFM and studied the effect of nanoscale wear on topography measurement. It was found that the resolution of amplitude modulation AFM measurements could be correlated to tip size and this relationship was also affected by the deformation of the materials. This research provides important insights into the fundamental mechanisms of nanoscale wear, which will lead to a better understanding of this technologically important phenomenon that controls the failure of systems from the macroscale to the nanoscale, with substantial economic, energetic, and environmental impacts.
Methyl Fumarate‐Derived Iron Carbonyl Complexes (FumET‐CORMs) as Powerful Anti‐inflammatory Agents

Autoimmune diseases are characterized by dendritic cell (DC)‐driven activation of pro‐inflammatory T cell responses. Therapeutic options for these severe diseases comprise small molecules such as dimethyl fumarate, or “gasotransmitters” such as CO. Herein we describe the synthesis of bifunctional enzyme‐triggered CO‐releasing molecules (ET‐CORMs) that allow the simultaneous intracellular release of both CO and methyl fumarate. Using bone‐marrow‐derived DCs the impressive therapeutic potential of these methyl fumarate‐derived compounds (FumET‐CORMs) is demonstrated by strong inhibition of lipopolysaccharide‐induced pro‐inflammatory signaling pathways and blockade of downstream interleukin‐12 or ‐23 production. The data also show that FumET‐CORMs are able to transform DCs into an anti‐inflammatory phenotype. Thus, these novel compounds have great clinical potential, for example, for the treatment of psoriasis or other inflammatory conditions of the skin.
Chemotherapy and terminal skeletal muscle differentiation in WT1‐mutant Wilms tumors

Wilms tumors (WT) with WT1 mutations do not respond well to preoperative chemotherapy by volume reduction, suggesting resistance to chemotherapy. The histologic pattern of this tumor subtype indicates an intrinsic mesenchymal differentiation potential. Currently, it is unknown whether cytotoxic treatments can induce a terminal differentiation state as a direct comparison of untreated and chemotherapy‐treated tumor samples has not been reported so far. We conducted gene expression profiling of 11 chemotherapy and seven untreated WT1‐mutant Wilms tumors and analyzed up‐ and down‐regulated genes with bioinformatic methods. Cell culture experiments were performed from primary Wilms tumors and genetic alterations in WT1 and CTNNB1 analyzed. Chemotherapy induced MYF6 165‐fold and several MYL and MYH genes more than 20‐fold and repressed many genes from cell cycle process networks. Viable tumor cells could be cultivated when patients received less than 8 weeks of chemotherapy but not in two cases with longer treatments. In one case, viable cells could be extracted from a lung metastasis occurring after 6 months of intensive chemotherapy and radiation. Comparison of primary tumor and metastasis cells from the same patient revealed up‐regulation of RELN and TBX2, TBX4 and TBX5 genes and down‐regulation of several HOXD genes. Our analyses demonstrate that >8 weeks of chemotherapy can induce terminal myogenic differentiation in WT1‐mutant tumors, but this is not associated with volume reduction. The time needed for all tumor cells to achieve the terminal differentiation state needs to be evaluated. In contrast, prolonged treatments can result in genetic alterations leading to resistance.