Miracle-dz/UniFAR-FTUs huggingface dataset:
Diseases of the mitochondrial DNA.

INTRODUCTION . _ . 1 175 THE HUMAN MITOCHONDRIAL DNA AND OXIDATIVE PHOSPHORYLATION 1176 Mitochondrial Biogenesis . 1 176 Mitochondrial OXPHOS Complexes and their Synthesis 1 178 Developmental Regulation of Nuclear OXPHOS Genes 1179 Mitochondrial DNA Genetics 1 1 8 1 MITOCHONDRIAL DNA MUTATIONS AND DISEASE. 1 183 Missense Mutations 1184 Biogenesis Mutations 1 1 88 Insertion-Deletion Mutations . 1 192 Copy Number Mutations 1 195 DEFECTS IN NUCLEAR-CYTOPLASMIC INTERACTIONS . 1 195 THE PROGRESSION OF OXPHOS DISEASES AND AGING 1 196 EVIDENCE FOR OXPHOS DEFECTS IN COMMON DEGENERATIVE DISEASES . 1201 METABOLIC AND GENETIC THERAPY OF OXPHOS DEFECTS 1206
Prognostic Significance of Pre- and Postoperative Serum Carcinoembryonic Antigen Levels in Patients with Colorectal Cancer

Background: To evaluate the prognostic significance of pre- and postoperative serum carcinoembryonic antigen(CEA) levels in colorectal cancer (CRC) patients. Methods: 425 CRC patients underwent curative resection at our institution. Their pre- and postoperative serum CEA level was classified into two groups according to concentration: normal CEA (<5.0 ng/ml) and abnormal CEA (≧5.0 ng/ml). Results: Of all patients, abnormal pre- and postoperative serum CEA levels were observed in 181 (42.6%) and 48 (11.3%) patients, respectively. Abnormal preoperative serum CEA level was significantly correlated with the tumor located in the colon, the depth of tumor invasion, the status of lymph node metastasis, UICC stage, and the presence of postoperative relapse (p < 0.05). Concurrently, an abnormal postoperative serum CEA level was also prominently related to the above corresponding parameters (p < 0.05), except for the tumor location. Patients with a failed conversion of abnormal preoperative value to normal postoperative concentration were found to have the worst overall survival rate. Abnormal pre- and postoperative serum CEA levels were single independent predictors for survival and postoperative relapse, respectively. Conclusions: The identification of abnormal pre- and postoperative serum CEA levels may be useful in the auxiliary cancer prognosis or postoperative surveillance of CRC patients.
Cerebral Glucose Metabolism and Sedation in Brain-injured Patients: A Microdialysis Study

Background: Disturbed brain metabolism is a signature of primary damage and/or precipitates secondary injury processes after severe brain injury. Sedatives and analgesics target electrophysiological functioning and are as such well-known modulators of brain energy metabolism. Still unclear, however, is how sedatives impact glucose metabolism and whether they differentially influence brain metabolism in normally active, healthy brain and critically impaired, injured brain. We therefore examined and compared the effects of anesthetic drugs under both critical (<1 mmol/L) and noncritical (>1 mmol/L) extracellular brain glucose levels. Methods: We performed an explorative, retrospective analysis of anesthetic drug administration and brain glucose concentrations, obtained by bedside microdialysis, in 19 brain-injured patients. Result: Our investigations revealed an inverse linear correlation between brain glucose and both the concentration of extracellular glutamate (Pearson r=−0.58, P=0.01) and the lactate/glucose ratio (Pearson r=−0.55, P=0.01). For noncritical brain glucose levels, we observed a positive linear correlation between midazolam dose and brain glucose (P<0.05). For critical brain glucose levels, extracellular brain glucose was unaffected by any type of sedative. Conclusions: These findings suggest that the use of anesthetic drugs may be of limited value in attempts to influence brain glucose metabolism in injured brain tissue.
A Mathematical and Physical Base for "A Standard Model of the Mind"

This paper describes a mathematical and physical base for "A Standard Model of the Mind. " It is a super-Turing model constrained by physical reality of the brain's construction. The constraints are noise and quantized charge transfer. The model has computing power beyond the Universal Turing Machine (UTM), which Turing himself claimed to be insufficient to model the brain. The super-Turing model meets Turing's desire for a more complex model. Allen Newell expressed difficulties in modelling the brain with the UTM not being as computationally complex as his functional analysis indicated. We will describe the model and note neuron operations compatible with it. Because of mathmatical idealities in both Turing and super-Turing models, physical devices cannot directly implement either model. However, both Turing machines and super-Turing models can point the direction to the design and operation of physical devices. Brain modeling should use the more powerful super-Turing model to describe its operation. Our research seeks to develop artificial neural networks based on this model. The super-Turing model is guiding analog- and digital-hybrid hardware development of these neural networks. We will describe the progress on an optical implementation with encouraging, chaos-mimicking results and on designs for an electronic implementation. We describe a possible spectrum of super-Turing inspired devices. We will call on the community to help further the devices and their use in 'A Standard Model of the Mind'.
A large-scale longitudinal study of flaky tests

Flaky tests are tests that can non-deterministically pass or fail for the same code version. These tests undermine regression testing efficiency, because developers cannot easily identify whether a test fails due to their recent changes or due to flakiness. Ideally, one would detect flaky tests right when flakiness is introduced, so that developers can then immediately remove the flakiness. Some software organizations, e.g., Mozilla and Netflix, run some tools—detectors—to detect flaky tests as soon as possible. However, detecting flaky tests is costly due to their inherent non-determinism, so even state-of-the-art detectors are often impractical to be used on all tests for each project change. To combat the high cost of applying detectors, these organizations typically run a detector solely on newly added or directly modified tests, i.e., not on unmodified tests or when other changes occur (including changes to the test suite, the code under test, and library dependencies). However, it is unclear how many flaky tests can be detected or missed by applying detectors in only these limited circumstances. To better understand this problem, we conduct a large-scale longitudinal study of flaky tests to determine when flaky tests become flaky and what changes cause them to become flaky. We apply two state-of-theart detectors to 55 Java projects, identifying a total of 245 flaky tests that can be compiled and run in the code version where each test was added. We find that 75% of flaky tests (184 out of 245) are flaky when added, indicating substantial potential value for developers to run detectors specifically on newly added tests. However, running detectors solely on newly added tests would still miss detecting 25% of flaky tests. The percentage of flaky tests that can be detected does increase to 85% when detectors are run on newly added or directly modified tests. The remaining 15% of flaky tests become flaky due to other changes and can be detected only when detectors are always applied to all tests. Our study is the first to empirically evaluate when tests become flaky and to recommend guidelines for applying detectors in the future.
Vitamin D Status and Mitochondrial Function in Children

Objective: Mitochondrial dysfunction is likely to be determined by vitamin D deficiency. The aim of this study is to assess the association between mitochondrial function and Vitamin D level in children. Patients and methods: This study was a prospective study conducted in primary school children in Mosul city. The study included 300 children, with an age ranged from 6 to 12 years. Serum 25(OH) D was analyzed and mitochondrial function was evaluated by measurement of serum lactate, pyruvate Lactate and L-Carnitine Results: Serum lactate, serum pyruvate and the lactate/ pyruvate ratio increased significantly (p ranged between .0001- .026) in children with insufficient vitamin D level (12-19 ng/ml) compared to those with sufficient vitamin D values (20-100 ng/ml). There was significant elevation in serum lactate, serum pyruvate and lactate/pyruvate ratio (p 100 ng /ml), there was significant elevation in serum lactate, lactate/pyruvate ratio (p 100 ng/ml is associated with abnormal mitochondrial function
The Validation of Direct and Meta Versions of the Coach–Athlete Relationship Questionnaire (ArCART-Q) in the Arabic Language: Their Relationship to Athlete’s Satisfaction with Individual Performance

Abstract Background: The first aim of this study is to achieve validation of the direct and meta-perspective versions of the Coach–Athlete Relationship Questionnaire in the Arabic language, and the second aim of this study is to determine the quality of the coach-athlete relationship to athlete’ satisfaction with individual performance according to sport participation type, sport duration, and sport achievement. Methods: A total of 259 athletes with a mean age of 22 years were recruited from various athletic clubs in Kuwait. Participants completed The Coach–Athlete Relationship Questionnaire and The Athlete Satisfaction Questionnaire. For this study, the factorial structure of the Arabic version of the Coach–Athlete Relationship Questionnaire (CART-Q) was used in Kuwait and was prepared with both direct and meta perspectives. Results: The results of this study show evidence of the validity of the direct and meta-perspective Arabic versions of the CART-Q. The fit indices of the data collected by direct-method were as follows (x2/df = 2.21; RMSEA = 0.06; CFI = 0.98; GFI = 0.95; AGFI = 0.91); data for the meta-method were as follows (x2/df = 2.32; RMSEA = 0.08; CFI = 0.99; GFI = 0.93; AGFI = 0.87). Female participants have obtained higher means than males from all questionnaires. Conclusions: The results of the present study could help coaches and athletes from the Middle East to understand the reasons and methods that lead to a quality coach–athlete relationship.
Effect of the Dry-Cured Fermented Sausage “Salchichón” Processing with a Selected Lactobacillus sakei in Listeria monocytogenes and Microbial Population

In the present work, the effect of processing of dry-cured fermented sausage “salchichón” spiked with the selected Lactobacillus sakei 205 was challenge-tested with low and high levels of L. monocytogenes. The evolution of the natural microbial population throughout the “salchichón” ripening was also evaluated. For this, a total of 150 “salchichón” were elaborated and divided into six equal cases which were inoculated with different levels of L. monocytogenes, and L. sakei 205. Afterwards, sausages were ripened for 90 days according to a typical industrial process. Moisture content (%) and water activity (aw) decreased throughout the ripening up to values around 26% and 0.78, respectively. No differences for moisture content, aw, pH, NaCl and nitrite concentration were observed between the analyzed cases. Lactic acid bacteria counts in the L. sakei 205 inoculated cases were always higher than 6 log CFU g−1 during ripening. Enterobacteriaceae counts were reduced during ripening until non-detectable levels at the end of processing. Reductions in L. monocytogenes counts ranged from 1.6 to 2.2 log CFU g−1; therefore, the processing of “salchichón” itself did not allow the growth of this pathogen. Reduction in L. monocytogenes was significantly higher in the cases inoculated with L. sakei 205.
Social complexity and the fractal structure of group size in primate social evolution

Compared to most other mammals and birds, anthropoid primates have unusually complex societies characterised by bonded social groups. Among primates, this effect is encapsulated in the social brain hypothesis: the robust correlation between various indices of social complexity (social group size, grooming clique size, tactical behaviour, coalition formation) and brain size. Hitherto, this has always been interpreted as a simple, unitary relationship. Using data for five different indices of brain volume from four independent brain databases, we show that the distribution of group size plotted against brain size is best described as a set of four distinct, very narrowly defined grades which are unrelated to phylogeny. The allocation of genera to these grades is highly consistent across the different data sets and brain indices. We show that these grades correspond to the progressive evolution of bonded social groups. In addition, we show, for those species that live in multilevel social systems, that the typical sizes of the different grouping levels in each case coincide with different grades. This suggests that the grades correspond to demographic attractors that are especially stable. Using five different cognitive indices, we show that the grades correlate with increasing social cognitive skills, suggesting that the cognitive demands of managing group cohesion increase progressively across grades. We argue that the grades themselves represent glass ceilings on animals' capacity to maintain social and spatial coherence during foraging and that, in order to evolve more highly bonded groups, species have to be able to invest in costly forms of cognition.
The algebraic dynamics of generic endomorphisms of ℙn

We investigate some general questions in algebraic dynamics in the case of generic endomorphisms of projective spaces over a field of characteristic zero. The main results that we prove are that a generic endomorphism has no non-trivial preperiodic subvarieties, any infinite set of preperiodic points is Zariski dense and any infinite subset of a single orbit is also Zariski dense, thereby verifying the dynamical "Manin--Mumford" conjecture of Zhang and the dynamical "Mordell--Lang" conjecture of Denis and Ghioca--Tucker in this case.
The cooperative array performance experiment: A joint China-US vector field experiment.

The cooperative array performance experiment (CAPEx) was performed in Lake Washington near Seattle in September 2009. Acoustic transmissions in the 1.5–4 kHz band were recorded simultaneously on two vertical arrays: one a conventional 32‐element pressure‐sensor array and the other an 8‐element array that measured both pressure and the three orthogonal components of acoustic particle velocity at each element. The present talk is an overview of both the data collected and the hardware used during CAPEx. Data were collected on the stationary arrays for both stationary‐ and towed‐source scenarios in water 60 m deep. The source‐receiver range varied between 10 m and 4 km. The data collected at short range demonstrate the relationship between the pressure and particle velocity fields. At more distant ranges, the particle velocity data are used to estimate the bearing to the source. Experimental results are compared to predictions generated using numerical models. [Work supported by ONR. ]
MagCode: NFC-Enabled Barcodes for NFC-Disabled Smartphones

Mobile payment has achieved explosive growth in recent years due to its contactless feature, which lowers the infection risk of COVID-19. In the market, near-field communication (NFC) and barcodes have become the de facto standard technologies for mobile payment. The NFC-based payment outperforms barcode-based payment in terms of security, usability, and convenience. It is especially more user-friendly for the amblyopia group. Unfortunately, NFC functionality is unavailable in nearly half of smartphones in the market nowadays due to the shortage of NFC modules or being disabled for security reasons. In this work, we present MagCode, a cross-technology communication between an NFC reader and a camera, which allows customers to enjoy the high security and convenience of NFC-based payment and the pervasiveness of cameras. At the heart of MagCode is the harmless magnetic interference on the CMOS image sensor of a smartphone placed nearby the NFC reader, resulting in a group of barcode-like stripes appearing on the captured images. We take advantage of these stripes to encode the data and achieve simplex communication from an NFC reader to an NFC-denied or NFC-disabled smartphone. In particular, we design and implement a stack of protocols from the physical to the transport layer and test the proof-of-concept prototype across 11 smart devices. Extensive evaluations demonstrate a maximum throughput of 2.58 kbps, which outperforms the magnetometer-based solution by 58×. It takes 1.8 seconds on average to accomplish the data exchange between an NFC reader to a smartphone in relation to mobile payments.
Nonlinear Feature Aggregation: Two Algorithms driven by Theory

Many real-world machine learning applications are characterized by a huge number of features, leading to computational and memory issues, as well as the risk of overfitting. Ideally, only relevant and non-redundant features should be considered to preserve the complete information of the original data and limit the dimensionality. Dimensionality reduction and feature selection are common preprocessing techniques addressing the challenge of efficiently dealing with high-dimensional data. Dimensionality reduction methods control the number of features in the dataset while preserving its structure and minimizing information loss. Feature selection aims to identify the most relevant features for a task, discarding the less informative ones. Previous works have proposed approaches that aggregate features depending on their correlation without discarding any of them and preserving their interpretability through aggregation with the mean. A limitation of methods based on correlation is the assumption of linearity in the relationship between features and target. In this paper, we relax such an assumption in two ways. First, we propose a bias-variance analysis for general models with additive Gaussian noise, leading to a dimensionality reduction algorithm (NonLinCFA) which aggregates non-linear transformations of features with a generic aggregation function. Then, we extend the approach assuming that a generalized linear model regulates the relationship between features and target. A deviance analysis leads to a second dimensionality reduction algorithm (GenLinCFA), applicable to a larger class of regression problems and classification settings. Finally, we test the algorithms on synthetic and real-world datasets, performing regression and classification tasks, showing competitive performances.
GoRec: A Generative Cold-start Recommendation Framework

Multimedia-based recommendation models learn user and item preference representation by fusing both the user-item collaborative signals and the multimedia content signals. In real scenarios, cold items appear in the test stage without any user interaction record. How to perform cold item recommendation is challenging as the training items and test items have different data distributions. These hybrid preference representations contained auxiliary collaborative signals, so current solutions designed alignment functions to transfer learned hybrid preference representations to cold items. Despite the effectiveness, we argue that they are still limited as these models relied heavily on the manually carefully designed alignment functions, which are easily influenced by the limited item records and noises in the training data. To tackle the above limitations, we propose a Generative cold-start Recommendation (GoRec) framework for multimedia-based new item recommendation. Specifically, we design a Conditional Variational AutoEncoder~(CVAE) based method that first estimates the underlying distribution of each warm item conditioned on the multimedia content representation. Then, we propose a uniformity-enhanced optimization objective to ensure the latent space of CVAE is more distinguishable and informative. In the inference stage, a generative approach is designed to obtain warm-up new item representations from the latent distribution. Please note that GoRec is applicable to arbitrary recommendation backbones. Extensive experiments on three real datasets and various recommendation backbones verify the superiority of our proposed framework. The code is available at https://github.com/HaoyueBai98/GoRec.
Functional stress responses in Glaucophyta: evidence of ethylene and ABA functions in C

Blue-green algae belonging to the monophyletic group Glaucophyta constitute an ancient 11 lineage that, along with Rhodophyta and Chloroplastida, is thought to have originated from a 12 primary endosymbiosis between cyanobacteria and a phagotrophic eukaryote (Price et al., 2016). 13 Today, 4 genera (Cyanophora, Gloeochaete, Cyanoptyche, and Glaucocystis) and 15 14 glaucophyte species are known. They are all unicellular freshwater phototrophs and are notably 15 characterized by non-stacked thylakoids and two unique traits inherited from a prokaryotic 16 ancestor: peptidoglycan layers around the plastid called muroplast or cyanelle in glaucophytes 17 and carboxysome-like bodies (Jackson et al., 2015; Price et al., 2016). For these reasons, 18 glaucophytes are sometimes called "living fossils," as they represent one of the earliest diverging 19 lineages within the Archaeplastida and retain traits of the cyanobacterial endosymbiont that are 20 absent in red or green algae. 21
Ultrasonic wave field determination of laser-acoustic sources with arbitrary shapes

Laser systems for excitation and detection of ultrasonic waves incorporate the benefits of a completely contact free method into ultrasonic NDT systems. Techniques using this huge potential were investigated for a long time but in most cases with focus on symmetric sources for surface waves. To study the material bulk properties strong and surface damaging laser pulses were necessary. However, by shortening the pulse length down to some nanoseconds and below one can excite ultrasonic waves in the bulk of the material without any damage. Important for ultrasonic testing methods is the shape of the ultrasonic field which is widely studied for simple geometries like point or line like sources but not for arbitrary intensity distributions in a general manner. The developed method offers to handle realistic source shapes which enables the link between the optical and acoustical design of contact free ultrasonic systems. Statement of Contribution and Methods: This work delivers valid arguments on improving the prediction of laser acoustic wave fields in the bulk of the medium towards a better understanding of the governing mechanisms. A hybrid point source synthesis HPSS is proposed combining laser beam profile and surface displacement measurements with the common algorithm behind a point source synthesis. Based on the calculated wave fields discretized in space and time the impact of asymmetries in the laser beam on the excited wave field is investigated. Results: Comparing idealized Gaussian shaped excitation to realistic laser intensity distribution reveals the dislocation of the center of the ultrasonic field. For both, the longitudinal and transversal acoustic wave, the natural focal dislocation increases with rising asymmetries of the laser beam profile.