Miracle-dz/UniFAR-FTUs huggingface dataset:
Zero-Shot Transfer of Protein Sequence Likelihood Models to Thermostability Prediction

Protein sequence likelihood models (PSLMs) are an emerging class of self-supervised deep learning algorithms which learn distributions over amino acid identities in structural and evolutionary contexts. Recently, PSLMs have demonstrated impressive performance in predicting the relative fitness of variant sequences without any task-specific training. In this work, we comprehensively analyze the capacity of six PSLMs to predict experimental measurements of thermostability for variants of hundreds of heterogeneous proteins. We assess performance of PSLMs relative to state-of-the-art supervised models, highlight relative strengths and weaknesses, and examine the complementarity between these models. We focus our analyses on stability engineering applications, assessing which methods and combinations of methods can most consistently identify and prioritize mutations for experimental validation. Our results indicate that structure-based PSLMs have competitive performance with the best existing supervised methods and can augment the predictions of supervised methods by integrating insights from their disparate training objectives.
Membangun koneksi matematis siswa dalam pemecahan masalah verbal

[Bahasa]: Penelitian ini mendeskripsikan proses membangun koneksi matematis dalam pemecahan masalah verbal atau soal cerita. Pada proses penyelesaian masalah verbal, diidentifikasi beberapa jenis koneksi yang dibangun siswa. Jenis soal dikembangkan berdasarkan karakteristik koneksi matematis menurut NCTM, yaitu koneksi antar topik matematika, koneksi dengan disiplin ilmu lain, dan koneksi dalam kehidupan sehari-hari. Pengumpulan data dilakukan melalui hasil kerja siswa dan wawancara semi terstruktur terhadap 2 orang subjek yang dipilih dengan tehnik purposive sampling. Penelitian ini mengunkap ada tujuh jenis koneksi yang dibangun oleh siswa pada saat menyelesaikan masalah verbal, yaitu: koneksi pemahaman, koneksi jika maka, koneksi representasi yang setara, koneksi hirarki, koneksi perbandingan melalui bentuk umum, koneksi prosedur, dan koneksi justifikasi dan representasi. Kata kunci: Koneksi Matematis; Pemecahan Masalah; Soal Verbal [English]: The current research aims to describe the process of developing mathematical connection in solving verbal or word mathematics problems. In solving problems, the mathematical connections developed by the subjects are identified. The mathematics problems refer to the characteristics of mathematical connections by NCTM, i.e. connections within mathematics topics, connection with other fileds, and connections with daily life. Data collection is conducted through students’ work and semi-structure interview with two subjects. The subjects are selected through purposive sampling. This research reveals seven kinds of mathematical connections developed by the subjects in solving verbal mathematics problems, i.e. connection in understanding, if then connection, equal representation connection, hierarchy connection, proportion connection through general form, procedure connection, and justification and representation connection. Keywords: Mathematical Connection; Problem Solving; Verbal Problems
Habitat structural complexity increases age-class coexistence and productivity in fish populations

Structurally-complex habitats harbour more taxonomically-diverse and more productive communities, a phenomenon generally ascribed to habitat complexity relaxing the strength of interspecific predation and competition. Here, we challenge this classical, community-centred view by showing that positive habitat complexity-productivity relationships may also emerge from between-age-class, intra-specific interactions at a single-population level. In replicated outdoor pond populations of the medaka fish ( Oryzias latipes ), structurally complex habitats provide refuges to newborns and relax the strength of cannibalism, resulting in increased survival of age-0+ individuals, in a 80 % increase in population growth rate, and in dampened negative density-dependence indicating elevated habitat carrying capacity. The resultant higher population density in complex habitats was associated with increased competition for food among age-0+ and age-1+ individuals, as revealed by their smaller and more variable body sizes. Positive habitat complexity-productivity relationships may thus be considered as a generally-emergent property of both size-structured communities and populations, in which a larger body size brings a predation advantage. Our results highlight that anthropogenic habitat simplification drives biodiversity loss not only from community-but also from population-level processes, and hence may further reduce population productivity in the surviving species. Enhancement of habitat structural complexity is therefore a pivotal action for biodiversity improvement, not only in the context of ecosystem management, but also for successful conservation of endangered populations.
Effects of sex and gonadal hormones on manually segmented hypothalamic and pituitary gland volumes in young healthy adults

The hypothalamus and pituitary regulate, amongst other functions, third order endocrine systems, and their volumes have been associated with normal and pathological outcomes. Yet, there are very few studies that examine their combined structural variations in vivo. This is due, in part, to their small size and a lack of comprehensive image segmentation protocols. In the current project we acquired high-resolution T1- (1mm isotropic) and T2-weighted (0.4mm in plane resolution) 3T magnetic resonance images (MRI) of the hypothalamus and pituitary gland, as well as salivary estradiol and testosterone from 31 (17M, 14F) young healthy adults. Women reported oral contraceptive use. Image preprocessing included non-uniformity correction, signal intensity normalization and standard stereotaxic space registration. We applied a comprehensive manual segmentation protocol of the whole hypothalamus, with detailed segmentation of the pituitary stalk, the anterior and posterior pituitary gland, and the posterior bright spot. We also propose a novel medial-lateral hypothalamic parcellation into medial preoptic, periventricular (PVN), and lateral hypothalamic regions. The protocol yielded good inter- (range: 0.78-0.92) and intra-rater (range: 0.79-0.94) Dice kappa overlap coefficients. We detected sex differences of the whole hypothalamus and each hemisphere, and a trend for the right preoptic region to be larger in males than in females, with a moderate effect size. Sex differences were maintained or enhanced when covarying for estradiol, but not when covarying for testosterone. In addition, testosterone was associated with the volume of the PVN, but only in women. In summary, these results suggest that there are morphometric differences at the level of the pituitary and hypothalamus that are likely driven by central regulation of gonadal hormones. The here described protocol allows the structural investigation of neuroendocrine effects in the central nervous system.
Fitness Tradeoffs of Multidrug Efflux Pumps in Escherichia coli K-12 in Acid or Base, and with Aromatic Phytochemicals

Multidrug efflux pumps are the frontline defense mechanisms of Gram-negative bacteria, yet little is known of their relative fitness tradeoffs under gut conditions such as low pH and the presence of antimicrobial food molecules. Low pH is important as it contributes to the proton-motive force (PMF) that drives most efflux pumps. We show how the PMF-dependent pumps AcrAB-TolC, MdtEF-TolC, and EmrAB-TolC undergo selection at low pH and in the presence of membrane-permeant phytochemicals. Competition assays were performed by flow cytometry of co-cultured Escherichia coli K-12 strains possessing or lacking a given pump complex. All three pumps showed negative selection under conditions that deplete PMF (pH 5.5 with CCCP, or at pH 8.0). At pH 5.5, selection against AcrAB-TolC was increased by aromatic acids, alcohols, and related phytochemicals such as methyl salicylate. The degree of fitness cost for AcrA was correlated with the phytochemical’s lipophilicity (logP). MdtEF-TolC and EmrAB-TolC each conferred a fitness cost at pH 5.5, but salicylate and benzoate conferred a net positive fitness contribution for the pump. Expression of pump genes was measured by digital PCR. Between pH 5.5 – 8.0, acrA and emrA were upregulated in log phase, whereas mdtE expression was upregulated in transition-to-stationary phase and at pH 5.5 in log phase. Methyl salicylate did not affect pump gene expression, despite selecting against AcrAB-TolC. Our results suggest that lipophilic non-acidic molecules select against a major efflux pump without positive section for others. IMPORTANCE For drugs that are administered orally, we need to understand how ingested phytochemicals modulate intrinsic drug resistance in our gut microbiome. Intrinsic drug resistance of bacteria is mediated by PMF-driven pumps that efflux many different antibiotics and cell waste products. These pumps play a key role in bacterial defense by conferring low-level resistance to antimicrobial agents at first exposure, while providing time for a pathogen to evolve resistance to higher levels of the antibiotic exposed. Nevertheless, efflux pumps confer energetic costs due to gene expression and pump energy expense. The bacterial PMF includes the transmembrane pH difference (ΔpH) which may be depleted by permeant acids and membrane disruptors. Understanding the fitness costs of efflux pumps may enable us to develop resistance breakers, that is, molecules that work together with antibiotics to potentiate their effect. We show that different pumps have distinct selection criteria, and we identified non-acidic aromatic molecules as promising candidates for drug resistance breakers.
On the Genus of the Moonshine Module

We provide a novel and simple description of Schellekens' seventy-one affine Kac-Moody structures of self-dual vertex operator algebras of central charge 24 by utilizing cyclic subgroups of the glue codes of the Niemeier lattices with roots. We also discuss a possible uniform construction procedure of the self-dual vertex operator algebras of central charge 24 starting from the Leech lattice. This also allows us to consider the uniqueness question for all non-trivial affine Kac-Moody structures. We finally discuss our description from a Lorentzian viewpoint.
Achieving Private Information Retrieval Capacity in Distributed Storage Using an Arbitrary Linear Code

We propose three private information retrieval (PIR) protocols for distributed storage systems (DSSs) where data is stored using an arbitrary linear code. The first two protocols, named Protocol 1 and Protocol 2, achieve privacy for the scenario with noncolluding nodes. Protocol 1 requires a file size that is exponential in the number of files in the system, while the file size required for Protocol 2 is independent of the number of files and is hence simpler. We prove that, for certain linear codes, Protocol 1 achieves the PIR capacity, i.e., its PIR rate (the ratio of the amount of retrieved stored data per unit of downloaded data) is the maximum possible for any given (finite and infinite) number of files, and Protocol 2 achieves the asymptotic PIR capacity (with infinitely large number of files in the DSS). In particular, we provide a sufficient and a necessary condition for a code to be PIR capacity-achieving and prove that cyclic codes, Reed-Muller (RM) codes, and optimal information locality local reconstruction codes achieve both the finite PIR capacity (i.e., with any given number of files) and the asymptotic PIR capacity with Protocols 1 and 2, respectively. Furthermore, we present a third protocol, Protocol 3, for the scenario with multiple colluding nodes, which can be seen as an improvement of a protocol recently introduced by Freij-Hollanti et al. We also present an algorithm to optimize the PIR rate of the proposed protocol. Finally, we provide a particular class of codes that is suitable for this protocol and show that RM codes achieve the maximum possible PIR rate for the protocol.
Open ocean fish cage and mooring system dynamics

To satisfy the global need for seafood, marine aquaculture is expected to play an increasing role as wild fish stocks decline. The expansion of near-shore aquaculture is becoming more difficult because of multi-use issues and environmental impact concerns. As a result, a national objective has been initiated to establish an open ocean aquaculture industry. To design and evaluate fish cages and moorings for the energetic open ocean requires a systematic approach utilizing physical and numerical modeling techniques. Using these methods, two robust fish cage and mooring systems were designed, deployed and have survived two New England winters. Prior to the second winter, the north system was refurbished and deployed with nine, 89 kN capacity load cells on the mooring and a six degree of freedom accelerometer motion package inside the fish cage. During the redeployment of the cage, open ocean drag tests were performed. A buoy was also deployed to measure the surface wave forcing. Assuming a linear system, a stochastic approach was used to analyze the load response of critical mooring lines and the motion response characteristics of the fish cage in heave, surge and pitch. Transfer functions were calculated for northeast storms. These normalized functions were compared with results of multiple physical and numerical model tests. The comparisons were used to validate the methods and to understand the dynamics of the deployed system so that future fish cage and moorings are designed and evaluated accurately to assist a new aquaculture industry to become economically feasible.
Immediate versus Delayed Umbilical Cord Clamping in Premature Neonates Born < 35 Weeks: A Prospective, Randomized, Controlled Study

The purpose of this study was to test whether delayed versus immediate cord clamping would result in higher blood pressure (BP) and hematocrit (Hct), and to assess its clinical effects on the neonatal course in premature neonates ( < 35 weeks). This was a prospective, masked, randomized, controlled study. Prior to delivery, 35 neonates were randomly assigned to immediate cord clamping (ICC) at 5 to 10 seconds, and a comparable group of 30 neonates were randomly assigned to delayed cord clamping (DCC) at 30 to 45 seconds. Intention-to-treat analyses revealed that the DCC group tended to have higher initial diastolic BP and higher Hct (especially in vaginally delivered neonates). Infants weighing < 1500 g with DCC tended to have higher mean BP, and needed less mechanical ventilation and surfactant compared with ICC neonates. Infants with DCC did not experience more polycythemia (Hct > 60%), but had a trend toward higher bilirubin levels with no differences in the phototherapy needs. DCC seems to be safe and may be beneﬁcial when compared with ICC in premature neonates. However, the differences between the two methods were modest and the clinical relevance needs to be assessed further by larger studies and additional meta-analysis of randomized trials.
Numerical approximation of higher-dimensional Continuum Dislocation Dynamics theory in single crystal plasticity

The model of elasto-plasticity that based on dislocation densities obtained from the higher-dimensional Continuum Dislocations Dynamics (hdCDD) theory was proposed. The hdCDD was reformulated and analyzed in a more precise mathematical setting. The representative slip planes were introduced and the micro structure behavior happened within this domain. The full setting were provided by embedding multiple of representative slip planes using RKDG into the elastic body using FEM.
Timing of Gestation after Bariatric Surgery: Should Women Delay Pregnancy for at Least 1 Postoperative Year?

Bariatric surgery is both a popular and highly effective treatment for obesity. Pregnancy after these procedures has proved safe, with certain gestational complication rates lower than those associated with pregnancy in the obese. Current recommendations suggest delaying pregnancy until after the ﬁrst postoperative year to avoid gestation during the rapid weight-loss phase. However, few controlled studies have examined the effects of postoperative pregnancy timing on gestational complications and outcomes. We discuss the current recommendations regarding timing of pregnancy after bariatric surgery. No conclusive evidence exists suggesting that pregnancy during the ﬁrst postoperative year is unsafe, although more research is needed. Future studies should examine the safety of early postoperative pregnancy and determine whether or not its gestational complication rates are lower than those associated with obesity. Until the inﬂuence of pregnancy timing on post–bariatric surgery perinatal outcomes is better understood, clinicians should take into account all relevant data, consult with their postoperative patients, and create reproductive timelines best suited to individual needs.
CFD ANALYSIS OF NON-LINEAR SLOSHING IN A CYLINDRICAL TANK

Present study involves CFD analysis of non-linear sloshing inside a partially filled cylindrical tank under harmonic excitation with two different frequencies using commercial software suite Fluidyn MP.Water-air interface is captured through volume of fluid (VOF) multiphase model using high resolution interface capturing scheme (HRIC). Flow is considered as laminar and full gravity model is implemented. Obtained numerical results in terms of wave height or sloshing height are compared with experimental values given by Yung Hsiang Chen et.al. [1]. Obtained numerical results for two different excitation frequencies are observed to be showing good qualitative and quantitative agreement with experimental results.
Anisotropic Scaling of Model Using Cage-Based Deformations

This paper proposes a method for anisotropically adjusting model size based on cage deformation technology. In this method, firstly the initial cage is constructed for the model according to the model features or the content definition. Then, the scale variations of each side of cage are adjusted in different directions by the minimum elastic energy method. Finally, the deformation result conforming to the model size adjustment constraints is calculated using the mean value coordinates. The result of the experiments on multiple different complexity models demonstrate that the proposed method can achieve anisotropic model size adjustment while maintaining the sensitivity features of the model.
Limit theorems for B–free integers and the Moebius function

This thesis presents several limit theorems linked by the topic of pseudorandomness of the Möbius function. The Möbius function is supported on the sequence of square–free integers. The distribution of square–free integers in short intervals was studied by Hall in a series of papers starting 1982. In particular, he provided the asymptotic order for the mean square of the number of square–free integers in a short interval and proved upper bounds for higher moments of the same variable. The first part of this thesis contains a generalization of Hall’s result on the mean square to a class of B–free integers under certain assumptions on the underlying set B. Additionally, we provide a weaker analogue of these results for the case of number fields. The second part of this thesis is concerned with the limiting distribution of two random variables with respect to a special class of logarithmic measures appearing in a study of the Mertens function. An adaptation of Erdős–Kac theorem to these measures is presented; more precisely, it is shown that the limiting distribution of the number of different prime factors of an integer with respect to our signed measures has a positive and a negative Gaussian parts. Further, the distribution of smooth integers in the same framework is studied. The limiting distribution in this case is also explicitly given and turns out to be intricately connected to the so-called generalized Dickman–de Bruijn distribution. Overall, the results presented in this thesis lead to a better understanding of statistics of several arithmetical sequences.
Advanced Maternal Age Is an Independent Risk Factor for Intrauterine Growth Restriction

Reports on the association between advanced maternal age (AMA) and intra-uterine growth restriction (IUGR) are conﬂicting. Our objective was to determine if AMA is an independent risk factor for IUGR. Our case-control study compared cases with IUGR (birthweight < 10th percentile for gestational age) and a control group without IUGR. Gestational ages were all conﬁrmed by ultrasound. The study included only singletons and fetal anomalies were excluded. Both groups were evaluated for maternal demographics and clinical risk factors. AMA was deﬁned as maternal age > 35 years. Univariate and multivariate analyses were used to examine associations. During the study period, there were 824 cases with IUGR meeting the inclusion criteria; these were compared with 1648 controls (no IUGR) randomly selected from the same population during the same study period. The signiﬁcant factors associated with IUGR multivariate analyses were black race (odds ratio [OR], 22.4; 95% conﬁdence interval [CI], 17.8 to 28); chronic hypertension (OR, 2.2; 95% CI, 1.5 to 3.2); pregestational diabetes (OR, 3.3; 95% CI, 1.6 to 7) illicit drug use (OR, 3.3; 95% CI, 2.2 to 5.2), and AMA (OR, 1.4; 95% CI, 1.1 to 1.8). There was a positive dose–response association between increasing maternal age and increasing risk for IUGR. At maternal age of 40 years or older, the OR and 95% CI for IUGR was 3.2 and 1.9 to 5.4, respectively. AMA is an independent risk factor for IUGR. Our ﬁndings suggest that screening for IUGR is indicated in women age 35 years or older
Neural Network and Regression Based Model for Cows’ Milk Yield Prediction in Different Climatic Gradients

The present study was designed to develop the prediction equations for 305 days fat corrected milk yield on the basis of part periods milk yield, milk component and conformation traits of multigenotype cows. Artificial Neural Network model had the best prediction accuracy across varying environments, though Genetic Function Algorithm had the overall best adequacy for fat corrected milk yield predictions (FCM305d=1036.1-98.3RP+22FY+15.92UC-0.07RUH; Adj R=0.997; RMSE=30.07; BIC=1997.28).
Exposure to Mercury during the First Six Months via Human Milk and Vaccines: Modifying Risk Factors

Breastfeeding is the best natural protection infants have against morbidity and mortality, and the development of safe and effective vaccines has made it possible to immunize children against infectious disease. Both of these mechanisms for ensuring good health in children may be compromised by contact with mercury (Hg). Maternal exposure to environmental Hg during pregnancy can predispose nursing children to neurodevelopmental disorders. Despite the World Health Organization assurance that thimerosal-preserved vaccines are safe to use in infants, the United States, the European Union, and dozens of other countries have eliminated thimerosal as a vaccine preservative and stopped the immunization of children with such vaccines. Because of the increase in environmental pollution and the need to produce cheap and safe vaccines, there is a need to address the uncertainty of vaccine-ethylmercury risk of toxicity and Hg exposure during breastfeeding.
ON MIXED PRODUCT OF n BOOLEAN ALGEBRAS

0« In [2] J . Pionka introduced the notion of nixed product of Boolean algebras B^Bg.B^ and he described the equational c l a s s generated by a l l such produots* In t h i s paper we genera l ise the notion of mixed product f o r n Boolean algebras B ^ f B 2 , . f B n , n ^ 3 and we give a f i n i t e axiomatics f o r the equat ional c l a s s 0Cfl generated by a l l algebras being such productB. Moreover we w i l l show tha t the o lass X, oan be obtained n by taking mixed subproduots of n Boolean algebras (and t h e i r isomorphic copies only) .