Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization of Ultrahigh-Throughput Screening Assay for Protein Engineering of d-Allulose 3-Epimerase

d-Allulose is the corresponding epimer of d-fructose at the C-3 position, which exhibits a similar taste and sweetness to sucrose. As a low-calorie sweetener, d-allulose has broad application prospects in the fields of medicine, food, and so on. Currently, the production method of d-allulose is mainly the enzymatic conversion of d-fructose by d-allulose 3-epimerase (DAEase). However, the limited specific activity and thermal stability of DAEase restrict its industrial application. Herein, an ultrahigh-throughput screening assay based on the transcription factor PsiR was extensively optimized from the aspects of culture medium components, screening plasmid, and expression host, which enhanced the correction between the fluorescent readout and the enzyme activity. Then, the error-prone PCR (epPCR) library of Clostridium cellulolyticum H10 DAEase (CcDAEase) was screened through the above optimized method, and the variant I228V with improved specific activity and thermal stability was obtained. Moreover, after combining two beneficial substitutions, D281G and C289R, which were previously obtained by this optimized assay, the specific activity of the triple-mutation variant I228V/D281G/C289R reached up to 1.42-fold of the wild type (WT), while its half-life (T1/2) at 60 °C was prolonged by 62.97-fold. The results confirmed the feasibility of the optimized screening assay as a powerful tool for the directed evolution of DAEase.
APPROACHES TO MODEL TRANSFERABILITY AND UPDATING: THE COMBINED TRANSFER ESTIMATOR

The idea of model transferability is to use previously estimated model parameters from a different area for model estimation. The combined transfer estimator is based on the mean squares error criterion and extends the Bayesian procedure to explicitly account for the presence of a transfer bias. The suggested estimator is easy to apply because it is expressed as a linear combination of the direct estimation results and the previously estimated parameters. The combined estimator is shown to have superior accuracy in a mean square error sense to a direct (unbiased nontransfer) estimator whenever the transfer bias is relatively small. Numerical examples of the transfer region--where the combined estimator is superior to the direct estimator--are provided.
Current Role of Non-Elective Transnasal Endoscopic Surgery: our Experience and Review of The Literature

Background: in the last 30 years Trans-Nasal Endoscopic Surgery (TNES) has emerged as the mainstay of the elective treatment of most pathologies arising from sinonasal cavities. Growing technology and techniques made TNES an essential instrument even in the emergency/urgency scenario. Materials and Methods: a retrospective cohort analysis was conducted at our tertiary care center including patients who required TNES within 48 hours from their admission at the Emergency Department. Demographic characteristics and surgical outcomes were evaluated for patients treated from 1st January 2016 and 31th December 2020. Moreover, we reviewed the most recent literature about safety and efficacy of non-elective TNES in the management of the commonest otorhinolaryngology emergencies: epistaxis, acute bacterial rhinosinusitis, acute invasive fungal rhinosinusitis, and post-traumatic optic neuropathy. Results: on the whole, we performed non-elective TNES in 45 patients, with a success and a complication rate of 93.3% and 0.0%, respectively. 11.1% of patients reported long-term sequelae related to their primary disease, in spite of treatment. No deaths were perioperatively reported. 52 studies about non-elective TNES were included in the present paper, each encompassing one single disease. Conclusion: the specific competences acquired by otorhinolaryngologists made TNES a safe and efficacious procedure even in the treatment of non-elective sinonasal diseases. The importance of a well-trained multidisciplinary team came to light for a prompt and correct management of sinonasal conditions that are barely rare but potentially sight- and life-threatening.
Energy-dependent ~100 μs Time Lags as Observational Evidence of Comptonization Effects in the Neutron Star Plasma Environment

We present a Comptonization model for the observed properties of the energy-dependent soft/hard time lags and pulsed fraction (amplitude) associated with the pulsed emission of a neutron star (NS). We account for the soft lags by downscattering of hard X-ray photons in the relatively cold plasma of the disk or NS surface. A fraction of the soft X-ray photons coming from the disk or NS surface upscatter off hot electrons in the accretion column. This effect leads to hard lags as a result of thermal Comptonization of the soft photons. This model reproduces the observed soft and hard lags due to the down- and upscattered radiation as a function of the electron number densities of the reflector, n, and the accretion column, n. In the case of the accretion-powered millisecond pulsars IGR J00291+5934, XTE J1751-305, and SAX J1808.4-3658, the observed time lags agree well with the model. Soft lags are observed only if n ≪ n. Scattering of the pulsed emission in the NS environment may account for the observed time lags as a nonmonotonic function of energy. The time lag measurements can be used as a probe of the innermost parts of the NS and accretion disk. We determine the upper and lower limits of the density variation in this region using the observed time lags. The observed energy-dependent pulsed amplitude allows us to infer a variation of the Thomson optical depth of the Compton cloud in which the accretion column is embedded.
Non-linear acoustic waves in discs

Une equation d'onde est etablie et utilisee pour calculer les profils et les forces des chocs pour des ondes acoustiques dans des disques, et pour calculer les taux d'ecoulement du gaz. Les resultats numeriques sont compares a ceux de Spruit H.C. (1987, Astron. Astrophys., 184).
Open-ended Knowledge Tracing for Computer Science Education

In educational applications, knowledge tracing refers to the problem of estimating students’ time-varying concept/skill mastery level from their past responses to questions and predicting their future performance.One key limitation of most existing knowledge tracing methods is that they treat student responses to questions as binary-valued, i.e., whether they are correct or incorrect. Response correctness analysis/prediction is straightforward, but it ignores important information regarding mastery, especially for open-ended questions.In contrast, exact student responses can provide much more information.In this paper, we conduct the first exploration int open-ended knowledge tracing (OKT) by studying the new task of predicting students’ exact open-ended responses to questions.Our work is grounded in the domain of computer science education with programming questions. We develop an initial solution to the OKT problem, a student knowledge-guided code generation approach, that combines program synthesis methods using language models with student knowledge tracing methods. We also conduct a series of quantitative and qualitative experiments on a real-world student code dataset to validate and demonstrate the promise of OKT.
Will knowing more English reduce the perceptual illusions in Mandarin Chinese?

: Word-medial consonant clusters (e.g. /ʃp/ in ‘dishpan’) are illicit in Mandarin Chinese. When Mandarin listeners perceive this sound sequence, it has been claimed that their speech perception processes will ‘repair’ it by adding an illusory medial vowel /i/. In an AX discrimination task (where participants decide whether two stimuli are the same or di�erent), we ask whether the knowledge of a language with a less restrictive phonotactic system, in this study, English, will reduce the perceptual illusions resulting from the knowledge of a language with a more restrictive phonotactic system, Mandarin. Critical trials have a short vowel [i] or [y] and a long vowel with the same quality (/i/ or /y/). We predict that, for [y] trials, the perceptual repair process replaces [y] with /i/, leading to fewer incorrect ‘same’ responses; for [i] trials, [i] is replaced with /i/, leading to more incorrect ‘same’ responses. Critically, for [i] trials, the stronger perceptual repair process for Mandarin-dominant bilinguals will lead to more incorrect ‘same’ responses relative to English-dominant bilinguals. However, the results did not follow our predictions. There was no perceptual repair e�ect measured by the proportion of incorrect ‘same’ response of [i] trials over that of the control group, the [y] trials, and the degree of dominance in English was neither found to a�ect the results. We conclude by discussing directions for future research.
SRNIC: A Scalable Architecture for RDMA NICs

RDMA is expected to be highly scalable: to perform well in large-scale data center networks where packet losses are inevitable ( i.e. , high network scalability), and to support a large number of performant connections per server ( i.e. , high connection scalability). Commercial RoCEv2 NICs (RNICs) fall short on scalability as they rely on a lossless, limited-scale network fabric and support only a small number of performant connections. Recent work IRN improves the network scalability by relaxing the lossless network requirement, but the connection scalability issue remains unaddressed. In this paper, we aim to address the connection scalability challenge, while maintaining high performance and low CPU overhead as commercial RNICs, and high network scalability as IRN, by designing SRNIC, a Scalable RDMA NIC architecture. Our key insight in SRNIC is that, on-chip data structures and their memory requirements in RNICs can be minimized with careful protocol and architecture co-designs to improve connection scalability. Guided by this insight, we analyze all data structures involved in an RDMA conceptual model, and remove them as many as possible with RDMA protocol header modiﬁcations and architectural innovations, including cache-free QP scheduler and memory-free selective repeat. We implement a fully functional SRNIC prototype using FPGA. Experiments show that, SRNIC achieves 10K performant connections on chip and outperforms commercial RNICs by 18x in terms of normalized connection scalability ( i.e.
A short note on the concept of free choice

We argue that the concepts of "freedom of choice" and of "causal order" are intrinsically linked: a choice is considered "free" if it is correlated only to variables in its causal future. We discuss the implications of this to Bell-type scenarios, where two separate measurements are carried out, neither of which lies in the causal future of the other, and where one typically assumes that the measurement settings are chosen freely. Furthermore, we refute a recent criticism made by Ghirardi and Romano in [arXiv:1301.5040] and [arXiv:1302.1635] that we used an unphysical freedom of choice assumption in our previous works, [Nat. Commun. 2, 411 (2011)] and [Phys. Rev. Lett. 108, 150402 (2012)].
Immediate Implant Placement in Infected Sockets: Curettage Protocol Plus Disinfection with Hydrogen Peroxide and Rifamycin. Retrospective Analysis at 6 years of Follow-up

Context: Immediate implant placement in a fresh socket after extraction is an increasingly popular and established treatment option. However, active infection at the extraction site can adversely affect the outcome of this procedure. Aims: This study was designed to evaluate the clinical results of immediate dental implant placement in infected extraction sockets. Settings and Design: using a standardized protocol, which included the use of 3% hydrogen peroxide plus rifamycin 500 mg as irrigation for decontamination of the infected socket before implant insertion with submerged healing. Patients and methods: The sample consisted of 227 implants placed in 158 patients, the data were obtained through a retrospective review of the clinical registry selected of patients who received implants according to the protocol described. Statistical analysis used: A generalized binary response regression model was used. For all tests, the statistical significance value was set at p <0.05. Results: Of the 227 implants placed immediately in the infected sites using the described protocol with an average follow-up of 6 years of prosthetic loading, only 11 failed, resulting in a cumulative implant survival rate of 95.2%. Only the medical history / harmful habits factor (HM / HH) was significant (p = 0.002), in this group the success rate was 85.7%. However, in the group of healthy patients without harmful habits, the success rate rises to 98.8%. Conclusion: Immediate implant placement in infected sites using these protocols in healthy patients shows a survival rate similar to that published for implants placed in non-infected sites.
Contextualizing Language Models for Norms Diverging from Social Majority

To comprehensibly contextualize decisions, artificial systems in social situations need a high degree of awareness of the rules of conduct of human behavior. Especially transformer-based language models have recently been shown to exhibit some such awareness. But what if norms in some social setting do not adhere to or even blatantly deviate from the mainstream? In this paper, we introduce a novel mechanism based on deontic logic to allow for a flexible adaptation of individual norms by de-biasing training data sets and a task-reduction to textual entailment. Building on the popular ’Moral Stories’ dataset we on the one hand highlight the intrinsic bias of current language models, on the other hand characterize the adaptability of pre-trained models to deviating norms in fine-tuning settings. 1
Gallium Anomaly: critical view from the global picture of ν e and ¯ ν e disappearance

: The signiﬁcance of the Gallium Anomaly, from the BEST, GALLEX, and SAGE radioactive source experiments, is quantiﬁed using diﬀerent theoretical calculations of the neutrino detection cross section, and its explanation due to neutrino oscillations is compared with the bounds from the analyses of reactor rate and spectral ratio data, β decay data, and solar neutrino data. In the 3+1 active-sterile neutrino mixing scheme, the Gallium Anomaly is in strong tension with the individual and combined bounds of these data sets. In the combined scenario with all available data, the parameter goodness of ﬁt is below 0.042%, corresponding to a severe tension of 4–5 σ , or stronger. Therefore, we conclude that one should pursue other possible solutions beyond short-baseline oscillations for the Gallium Anomaly. We also present a new global ﬁt of ν e and ¯ ν e disappearance data, showing that there is a 2.6–3.3 σ preference in favor of short-baseline oscillations, which is driven by an updated analysis of reactor spectral ratio data.
Uncertainty and Sensitivity Analysis of Ground-Motions Simulation at Un- Instrumented Sites Using Gaussian Process Regression

Earthquake ground motion time series plays a critical role in the performance assessment of the structures, especially when nonlinear response history analysis for a specific structural system is required. The number of currently available recording instruments is sparse. Therefore, it is necessary to have a reliable methodology to construct the ground motion time series at the desired target un-instrumented sites. Using the Gaussian Process Regression (GPR), we recently presented an approach for generating ground motion time series at target sites where there are no available recording sensors. This model is trained based on physics-based simulated earthquake datasets in northern California and evaluated using the recorded motions during the 2019 M7.1 Ridgecrest earthquake sequence and 2020 M4.5 South El Monte datasets in Southern California. This GPR method interpolates the observed Discrete Fourier Transform (DFT) coefficients to construct the frequency-content of the ground motion at the target location and generate time series at the site. The optimized hyperparameter of the GPR model depends on the observation density of the training dataset. Thus, in this study, we tuned the hyperparameter of the GPR model based on observation density using the 2019 M7.1 Ridgecrest earthquake dataset recorded by the Community Seismic Network (CSN). In addition, we introduce a methodology to generate random realizations of ground motions using the trained GPR model at each target site. We utilize this methodology for the 2019 M7.1 Ridgecrest earthquake to conduct uncertainty quantification of the estimated motions at short and long periods. The results illustrate that uncertainty of the generated time series is lower for longer periods than that for shorter periods. In addition, we carried out the sensitivity analysis of both predictions’ error and uncertainty with respect to a variety of governing parameters such as density of the observations surrounding the target site and estimated uncertainty of the local site conditions. It is shown that the observation density plays a key role in both reducing the prediction error as well as the uncertainty of the estimation. Moreover, we studied the improvement of the performance of the GPR model in the prediction of ground motions for 2019 M7.1 Ridgecrest as well as the 2020 M4.5 South El Monte earthquakes recorded by the California Integrated Seismic Network (CISN) through feeding more observed motions from CSN sites to the model. The results illustrate that the prediction error decreases, especially for those target sites located inside the added observed network (CSN) boundary. However, the prediction uncertainty is not changed considerably, especially at short periods.
Candidate star clusters toward the inner Milky Way discovered on deep-stacked KS-band images from the VVV Survey

The census of star clusters in the inner Milky Way is incomplete because of extinction and crowding. We embarked on a program to expand the star cluster list in the direction of the inner Milky Way using deep stacks of Ks-band images from the VISTA Variables in Via Lactea (VVV) Survey. We applied an automated two-step procedure to the point-source catalog derived from the deep Ks images: first, we identified overdensities of stars, and then we selected only candidate clusters with probable member stars that match an isochrone with a certain age, distance, and extinction on the color-magnitude diagram. This pilot project only investigates the cluster population in part of one VVV tile, that is, b201. We identified nine cluster candidates and estimated their parameters. The new candidates are compact with a typical radius on the sky of ~0.2--0.4 arcmin (~0.4-1.6 pc at their estimated distances). They are located at distances of ~5-14 kpc from the Sun and are subject to moderate extinction of E(B-V)=0.4-1.0 mag. They are sparse, probably evolved, with typical ages log(t/1 yr)~9. Based on the locations of the objects inside the Milky Way, we conclude that one of these objects is probably associated with the disk or halo and the remaining objects are associated with the bulge or the halo. The cluster candidates reported here push the VVV Survey cluster detection to the limit. These new objects demonstrate that the VVV survey has the potential to identify thousands of additional cluster candidates. The sub-arcsec angular resolution nd the near-infrared wavelength regimen give it a critical advantage over other surveys.
Algorithmic Analysis of Code-Breaking Games

Code-breaking games are two-player games in which the first player selects a code from a given set and the second player strives to reveal it using a minimal number of experiments. A prominent example of a code-breaking game is the board game Mastermind, where the codebreaker tries to guess a combination of coloured pegs. There are many natural questions to ask about code-breaking games. What strategy for experiment selection should the codebreaker use? Can we compute a lower and upper bound for the number of experiments needed to reveal the code? Is it possible to compute an optimal strategy? What is the performance of a given heuristic? Much research on the topic has been done but the authors usually focus on one particular game and little has been written about code-breaking games in general. In this work, we create a general model of code-breaking games based on propositional logic and design a computer language for game specification. Further, we suggest general algorithms for game analysis and strategy synthesis and implement them in a computer program. Using the program, we can reproduce existing results for Mastermind, analyse new code-breaking games and easily evaluate new heuristics for experiment selection.
Comparison of hydrostatic weighing and plethysmography techniques for the development of skinfold prediction equations for children

Regression equations between skinfold (SKF) measurements and air displacement plethysmography (ADP) were determined 6 to 18 year old athletes (80 males / 34 females) using Pearson r correlation coefficients. Triceps and mid-calf SKF and percent body fat (%BF) by ADP were measured during an Athletic Ability Assessment at The HIT Center (Huntington, WV). A high relationship was found between SKF and %BF by ADP (males; r = .76, females; r = .74, all; r = .77). Data from the subjects were compared with similar correlations determined between SKF and %BF by hydrostatic weighing (HW) from another study (Slaugter et al., 1988). SKF showed a higher correlation with %BF by ADP than by HW (ADP, r = .77 and HW, r = .72). Therefore, the SKF regression equation based on % BF by ADP may be more accurate than the equation calculated in children for %BF by HW.
Dynamic Allocation of Reusable Resources: Logarithmic Regret in Overloaded Networks

We study the problem of dynamically allocating reusable resources to customers of n types. There are d pools of resources, and a ﬁnite number of units from each resource. If a customer request is accepted, the decision maker collects a type-dependent reward and the customer occupies, for a random service time, one unit from each resource in a set of these. This is a loss network: requests that are not accepted leave immediately. Upon service completion, these resource units become available for future allocation. The decision maker’s objective is to maximize the long-run average reward subject to the resource-capacity constraint. A natural linear programming (LP) relaxation of the problem serves as an upper bound on the performance of any policy. We identify a condition that generalizes the notion of overload in single-resource networks (i.e., when d = 1). The LP guides our construction of a threshold policy. In this policy, the number of thresholds equals the number of resource types (hence does not depend on the number of customer types). These thresholds are applied to a “corrected” headcount process. In the case of a single resource the corrected headcount is the same as headcount: the number of resource units that are occupied. We prove that in overloaded networks, the regret of this policy, benchmarked against the LP upper bound, is logarithmic in the total arrival volume in the many-customer many-resource-units asymptotic regime. No policy can achieve sub-logarithmic regret. Simulations showcase the performance of the proposed policy.