Miracle-dz/UniFAR-FTUs huggingface dataset:
Some new results in sequential Monte Carlo

Sequential Monte Carlo (SMC) methods have been well studied within the context of performing inference with respect to partially observed Markov processes, and their use in this context relies upon the ability to evaluate or estimate the likelihood of a set of observed data, given the state of the latent process. In many real-world applications such as the study of population genetics and econometrics, however, this likelihood can neither be analytically evaluated nor replaced by an unbiased estimator, and so the application of exact SMC methods to these problems may be infeasible, or even impossible. The models in many of these applications are complex, yet realistic, and so development of techniques that can deal with problems of likelihood intractability can help us to perform inference for many important yet otherwise inaccessible problems; this motivates the research presented within this thesis. The main focus of this work is the application of approximate Bayesian computation (ABC) methodology to state-space models (SSMs) and the development of SMC methods in the context of these ABC SSMs for filtering and smoothing of the latent process. The introduction of ABC here avoids the need to evaluate the likelihood, at the cost of introducing a bias into the resulting filtering and smoothing estimators; this bias is explored theoretically and through simulation studies. An alternative SMC procedure, incorporating an additional rejection step, is also considered and the novel application of this rejection-based SMC procedure to the ABC approximation of the SSM is considered. 5 This thesis will also consider the application of MCMC and SMC methods to a class of partially observed point process (PP) models. We investigate the problem of performing sequential inference for these models and note that current methods often fail. We present a new approach to smoothing in this context, using SMC samplers (Del Moral et al., 2006). This approach is illustrated, with some theoretical discussion, on a doubly stochastic PP applied in the context of finance.
Derivation of Annular Plate Sector Element for General Bending Analysis

A new mathematical finite element model suitable for the general bending analysis of annular plate structure is developed in polar coordinates system depending on the strain based approach has been derived. The element is simple and contains only the essential degrees of freedom. The element has 15 degrees of freedom, three at each node and satisfies the exact representation of the rigid body modes of displacement. The results obtained by using the proposed element in several numerical problems have shown that a rapid convergence to exact solution can be obtained with acceptable degree of accuracy when only few element are used. The element has the advantage over the other available annular plate elements. The improvement obtained is due to the fact that all the displacement fields of the present element satisfy the exact representation of rigid body modes of displacements then the shape function error due to rigid body modes becomes zero. Also, the present element satisfies the full geometry of the annular plate due to this point discretization error becomes zero. Finally the error due to strain mode becomes very small because the present element satisfies the compatibility equations of strains and the 12th coefficients of strain mode derived exactly from partial differential equations of strains. The numerical solution of several problems by using the present element proved to be powerful in the structural bending analysis of circular annular plates. Its results are better than the solution of other elements and packages with respect to analytical.
Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life

Significance Milk is fundamental for early life in mammals, providing nutrients and immunoregulatory compounds to developing young. Our study represents the largest mammalian milk microbiome survey to date. Across the mammalian tree of life, we show that lactating female mammals host a diverse collection of bacterial and archaeal taxa in their milk, representing one of the earliest exposures of mammalian young to the microbial world. The communities of microbes found within milks were largely a reflection of random, stochastic process. Nonetheless, milk microbiomes still showed signatures of selection that reflected the mother’s evolutionary history and ecology, including environment and diet. Milk microbiomes warrant study as the microbial species in milk likely colonize offspring guts and impact offspring physiology and behavior.
The Effectiveness of Rapid Syllable Transition Treatment in Improving Communication in Children with Cerebral Palsy: A Randomized Controlled Trial

ABSTRACT Cerebral palsy (CP) is a movement disorder and majority of children with CP have communication impairments which impact participation with this population. Rapid Syllable Transition Treatment (ReST) is a motor speech intervention primarily for children with Childhood Apraxia of Speech (CAS). A recent pilot study in which ReST was trialed with children with CP showed improved speech performance. Therefore, a single blind randomized controlled trial to compare ReST to usual care with 14 children with moderate-to-severe CP and dysarthria was conducted. ReST was provided on telehealth. ANCOVA with 95% confidence intervals indicated significant group differences in favor of ReST in speech accuracy (F = 5.1, p = .001), intelligibility (F = 2.8, p = .02) and communicative participation on both the FOCUS (F = 2, p = .02) and Intelligibility in Context Scale (F = 2.4, p = .04). ReST was found to be more effective than usual care.
Analysis of interface trap density of plasma post-nitrided Al2O3/SiGe MOS interface with high Ge content using high-temperature conductance method

The interface trap density (Dit) of SiGe metal-oxide-semiconductor (MOS) interfaces is analyzed by the conductance method to evaluate the effect of electron cyclotron resonance plasma post-nitridation on SiGe interfaces with various Ge compositions. We find that it is important to evaluate Dit of a high-Ge-content SiGe MOS interface by the conductance method to eliminate the effect of the large series resistance and capacitance due to the SiGe/Si hetero-interface. In conjunction with the high-temperature measurement in the conductance method, an equivalent circuit corresponding to the SiGe/Si hetero-interface enables us to eliminate the effect of the series resistance and capacitance of the hetero-interface. Thus, we successfully evaluated Dit at SiGe MOS interfaces with a Ge composition of up to 0.49 and the impact of plasma post-nitridation on the high-Ge-content SiGe interfaces. Although Dit increases with the Ge composition, plasma post-nitridation is effective even for a high-Ge-content SiGe interfac.
Computability equivalence of an extended Petri net model

The notion of computability has its origin in the works of the logicians Church, Gödel, Kleene, Post and Turing. Several approaches of computation were proposed: recursive functions, Post programs, lambda calculus, Turing machines, register machines, to mention some. It was shown that all these models were equivalent in terms of its computability power. In this paper a new computational paradigm called arithmetic Petri nets (APN) is introduced. APN are Petri nets with inhibitor arcs that perform three types of arithmetical operations; increment, decrement and test for zero. Its equivalence to Turing and therefore to all the other approaches was shown to be true by simulation of a register machine. In this paper a different path is proposed by first proving that all recursive functions are APN computable. The opposite implication is obtained from Kleene’s normal form theorem for APN . The normal form theorem was introduced by Kleene for the general recursive computation paradigm in terms of system of equations. The proof of Kleene’s normal form theorem for the APN computational paradigm is based on the idea of computation tree, where each node of such a tree will tell us how a value needed for the arithmetical operations can be inductively obtained. Then, using arithmetization plus course of value recursion a primitive recursive predicate is defined from which by means of a primitive recursive function the desired characterization for the value of the output function is established. 2142 Zvi Retchkiman Königsberg Mathematics Subject Classification: 03D78, 03D60, 03D20, 03D10
An inducible model of chronic hyperglycemia

ABSTRACT Transgene driven expression of Escherichia coli nitroreductase (NTR1.0) renders animal cells susceptible to the antibiotic metronidazole (MTZ). Many NTR1.0/MTZ ablation tools have been reported in zebrafish, which have significantly impacted regeneration studies. However, NTR1.0-based tools are not appropriate for modeling chronic cell loss as prolonged application of the required MTZ dose (10 mM) is deleterious to zebrafish health. We established that this dose corresponds to the median lethal dose (LD50) of MTZ in larval and adult zebrafish and that it induced intestinal pathology. NTR2.0 is a more active nitroreductase engineered from Vibrio vulnificus NfsB that requires substantially less MTZ to induce cell ablation. Here, we report on the generation of two new NTR2.0-based zebrafish lines in which acute β-cell ablation can be achieved without MTZ-associated intestinal pathology. For the first time, we were able to sustain β-cell loss and maintain elevated glucose levels (chronic hyperglycemia) in larvae and adults. Adult fish showed significant weight loss, consistent with the induction of a diabetic state, indicating that this paradigm will allow the modeling of diabetes and associated pathologies.
Englerin A Inhibits T-Type Voltage-Gated Calcium Channels at Low Micromolar Concentrations

Englerin A (EA) is a potent agonist of tetrameric transient receptor potential canonical (TRPC) ion channels containing TRPC4 and TRPC5 subunits. TRPC proteins form cation channels that are activated by plasma membrane receptors. They convert extracellular signals such as angiotensin II into cellular responses, whereupon Na+ and Ca2+ influx and depolarization of the plasma membrane occur. Via depolarization, voltage-gated Ca2+ (CaV) channels can be activated, further increasing Ca2+ influx. We investigated the extent to which EA also affects the functions of CaV channels using the high-voltage-activated L-type Ca2+ channel CaV1.2 and the low-voltage-activated T-type Ca2+ channels CaV3.1, CaV3.2, and CaV3.3. After expression of cDNAs in human embryonic kidney (HEK293) cells, EA inhibited currents through all T-type channels at half-maximal inhibitory concentrations (IC50) of 7.5 to 10.3 μM. In zona glomerulosa cells of the adrenal gland, angiotensin II-induced elevation of cytoplasmic Ca2+ concentration leads to aldosterone release. We identified transcripts of low- and high-voltage-activated CaV channels and of TRPC1 and TRPC5 in the human adrenocortical (HAC15) zona glomerulosa cell line. Although no EA-induced TRPC activity was measurable, Ca2+ channel blockers distinguished T- and L-type Ca2+ currents. EA blocked 60% of the CaV current in HAC15 cells and T- and L-type channels analyzed at −30 mV and 10 mV were inhibited with IC50 values of 2.3 and 2.6 μM, respectively. Although the T-type blocker Z944 reduced basal and angiotensin II-induced 24-hour aldosterone release, EA was not effective. In summary, we show here that EA blocks CaV1.2 and T-type CaV channels at low-micromolar concentrations. SIGNIFICANCE STATEMENT In this study we showed that englerin A (EA), a potent agonist of tetrameric transient receptor potential canonical (TRPC)4- or TRPC5-containing channels and currently under investigation to treat certain types of cancer, also inhibits the L-type voltage-gated Ca2+ (CaV) channel CaV1.2 and the T-type CaV channels CaV3.1, CaV3.2, and CaV3.3 channels at low micromolar concentrations.
Follicular fluid redox balance and DNA damage according to PCOS phenotype.

OBJECTIVE Classification of polycystic ovary syndrome (PCOS) according to their phenotypes is important in terms of understanding which parameter has clinical and laboratory implications. This study was designed to measure the follicular fluid total oxidant capacity (TOC) and total antioxidant capacity (TAC) and DNA degradation products of 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in patients with different PCOS phenotypes undergoing In-Vitro Fertilization/Intra-Cytoplasmic Sperm Injection (IVF/ICSI). PATIENTS AND METHODS Thirty women who were diagnosed with PCOS and twenty infertile patients who did not have the clinical and laboratory findings of PCOS were included. Women carrying at least two of the three parameters below were considered to have PCOS. (1) Biochemical or clinical manifestations of hyperandrogenism (HA); (2) Ovulatory dysfunction (OD); (3) Polycystic ovarian morphology (PCOM). Patients were then classified into four different PCOS phenotypes: (1) Phenotype A is also known as classical PCOS and meets all three criteria (HA/OD/PCOM). (2) Phenotype B has two criteria, HA and OD. (3) Phenotype C consists of HA and PCOM criteria. (4) Phenotype D is the non-hyperandrogenic form and consists of OD and PCOM criteria. Antagonist protocol was used in both PCOS and control groups. During oocyte pick-up, follicular fluid of the dominant follicle was collected. TAC and TOC levels, which are redox balance markers, and 8-OHdG levels, which are DNA degradation products, were measured in follicular fluid samples (FF). RESULTS Follicular fluid 8-OHdG levels of all four types of phenotypes were significantly higher than the control group. When the phenotype groups were evaluated among themselves, FF-8-OHdG levels of each group were found to be similar. Serum TOC levels of each phenotype group were found to be significantly higher than the control group. TAC levels of the patients in the control group were significantly higher than the other four phenotype groups. Oxidative stress index (OSI) values were significantly higher in all four phenotype groups compared to the control group. OSI values of phenotype B and D groups were significantly higher than phenotypes A and C. CONCLUSIONS In each phenotype of PCOS, TOC and OSI increased while TAC decreased. Increased OSI leads to DNA degradation and an increase in the level of 8-OHdG. The cumulative effect of oxidative stress and DNA degradation may be the main mechanism of PCOS-related subfertility.
Shaping the phycosphere: Analysis of the EPS in diatom‐bacterial co‐cultures

The phycosphere is a unique niche that fosters complex interactions between microalgae and associated bacteria. The formation of this extracellular environment, and the associated bacterial biodiversity, is heavily influenced by the secretion of extracellular polymers, primarily driven by phototrophic organisms. The exopolysaccharides (EPS) represent the largest fraction of the microalgae‐derived exudates, which can be specifically used by heterotrophic bacteria as substrates for metabolic processes. Furthermore, it has been proposed that bacteria and their extracellular factors play a role in both the release and composition of the EPS. In this study, two model microorganisms, the diatom Phaeodactylum tricornutum CCAP 1055/15 and the bacterium Pseudoalteromonas haloplanktis TAC125, were co‐cultured in a dual system to assess how their interactions modify the phycosphere chemical composition by analyzing the EPS monosaccharide profile released in the culture media by the two partners. We demonstrate that microalgal–bacterial interactions in this simplified model significantly influenced the architecture of their extracellular environment. We observed that the composition of the exo‐environment, as described by the EPS monosaccharide profiles, varied under different culture conditions and times of incubation. This study reports an initial characterization of the molecular modifications occurring in the extracellular environment surrounding two relevant representatives of marine systems.
USP14 inhibition regulates tumorigenesis by inducing apoptosis in gastric cancer

Deubiquitinases (DUBs) are an essential component of the ubiquitin-proteasome system (UPS). They trim ubiquitin from substrate proteins, thereby preventing them from degradation, and modulate different cellular processes. Ubiquitin-specific protease 14 (USP14) is a DUB that has mainly been studied for its role in tumorigenesis in several cancers. In the present study, we found that the protein levels of USP14 were remarkably higher in gastric cancer tissues than in the adjacent normal tissues. We also demonstrated that the inhibition of USP14 activity using IU1 (an USP14 inhibitor) or the inhibition of USP14 expression using USP14-specific siRNA markedly reduced the viability of gastric cancer cells and suppressed their migratory and invasive abilities. The reduction in gastric cancer cell proliferation due to the inhibition of USP14 activity was a result of the increase in the degree of apoptosis, as evidenced by the increased expression levels of cleaved caspase-3 and cleaved PARP. Furthermore, an experiment using the USP14 inhibitor IU1 revealed that the inhibition of USP14 activity suppressed 5-fluorouracil (5-FU) resistance in GC cells. Collectively, these findings indicate that USP14 plays critical roles in gastric cancer progression and suggest its potential to serve as a novel therapeutic target for gastric cancer treatment.
Assessment of generalised Bayesian structural equation models for continuous and binary data.

The paper proposes a novel model assessment paradigm aiming to address shortcoming of posterior predictive p $$ p $$ -values, which provide the default metric of fit for Bayesian structural equation modelling (BSEM). The model framework presented in the paper focuses on the approximate zero approach (Psychological Methods, 17, 2012, 313), which involves formulating certain parameters (such as factor loadings) to be approximately zero through the use of informative priors, instead of explicitly setting them to zero. The introduced model assessment procedure monitors the out-of-sample predictive performance of the fitted model, and together with a list of guidelines we provide, one can investigate whether the hypothesised model is supported by the data. We incorporate scoring rules and cross-validation to supplement existing model assessment metrics for BSEM. The proposed tools can be applied to models for both continuous and binary data. The modelling of categorical and non-normally distributed continuous data is facilitated with the introduction of an item-individual random effect. We study the performance of the proposed methodology via simulation experiments as well as real data on the 'Big-5' personality scale and the Fagerstrom test for nicotine dependence.
The extracellular matrix of green algae

Abstract Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.
Chronic Exposure to Environmentally Relevant Concentrations of Imidacloprid Impact Survival and Ecologically Relevant Behaviors of Fathead Minnow Larvae

Imidacloprid (IM) has emerged as a contaminant of concern in several areas within the United States due to its frequent detection in aquatic ecosystems and its pseudo‐persistence, which pose potential risks to nontarget species. We evaluated the sublethal toxicity of IM to fathead minnow larvae following chronic exposure beginning just after fertilization. Our in silico analysis and in vivo bioassays suggest that IM has a low binding affinity for the vertebrate nicotinate acetylcholine receptor (nAChR), as expected. However, chronic exposure to ≥0.16 µg IM/L reduced survival by 10%, and exposure to ≥18 µg IM/L reduced survival by approximately 20%–40%. Surviving fish exposed to ≥0.16 µg IM/L showed reduced growth, altered embryonic motor activity, and premature hatching. Furthermore, a significant proportion of fish exposed to ≥0.16 µg IM/L were slower to respond to vibrational stimuli and slower to swim away, indicating that chronic exposure to IM has the potential to impair the ability of larvae to escape predation. The adverse health effects we observed indicate that chronic exposure to environmentally relevant concentrations of IM may elicit sublethal responses that culminate in a significant increase in mortality during early life stages, ultimately translating to reduced recruitment in wild fish populations. Environ Toxicol Chem 2023;42:2184–2192. © 2023 SETAC
CACO: A Core-Attachment Method With Cross-Species Functional Ortholog Information to Detect Human Protein Complexes

Protein complexes play an essential role in living cells. Detecting protein complexes is crucial to understand protein functions and treat complex diseases. Due to high time and resource consumption of experiment approaches, many computational approaches have been proposed to detect protein complexes. However, most of them are only based on protein-protein interaction (PPI) networks, which heavily suffer from the noise in PPI networks. Therefore, we propose a novel core-attachment method, named CACO, to detect human protein complexes, by integrating the functional information from other species via protein ortholog relations. First, CACO constructs a cross-species ortholog relation matrix and transfers GO terms from other species as a reference to evaluate the confidence of PPIs. Then, a PPI filter strategy is adopted to clean the PPI network and thus a weighted clean PPI network is constructed. Finally, a new effective core-attachment algorithm is proposed to detect protein complexes from the weighted PPI network. Compared to other thirteen state-of-the-art methods, CACO outperforms all of them in terms of F-measure and Composite Score, showing that integrating ortholog information and the proposed core-attachment algorithm are effective in detecting protein complexes.
A differential Michelson interferometer with orthogonal single frequency laser for nanometer displacement measurement

A novel differential Michelson laser interferometer is proposed to eliminate the influence of environmental fluctuations for nanometer displacement measurement. This differential interferometer consists of two homodyne interferometers in which two orthogonal single frequency beams share common reference arm and partial measurement arm. By modulating the displacement of the common reference arm with a piezoelectric transducer, the common-mode displacement drift resulting from the environmental disturbances can be well suppressed and the measured displacement as differential-mode displacement signal is achieved. In addition, a phase difference compensation method is proposed for accurately determining the phase difference between interference signals by correcting the time interval according to the average speed in one cycle of interference signal. The nanometer displacement measurement experiments were performed to demonstrate the effectiveness and feasibility of the proposed interferometer and show that precision displacement measurement with standard deviation less than 1 nm has been achieved.