Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential L 1 regulation in pluripotent stem cells of humans and apes

Identifying cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic understanding of the evolution and diversity of our own species. Until now, preserved tissues have been the main source for most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behaviour and are not amenable to genetic manipulation. We propose that induced pluripotent stem (iPS) cells could be a unique biological resource to determine relevant phenotypical differences between human and NHPs, and that those differences could have potential adaptation and speciation value. Here we describe the generation and initial characterization of iPS cells from chimpanzees and bonobos as new tools to explore factors that may have contributed to great ape evolution. Comparative gene expression analysis of human and NHP iPS cells revealed differences in the regulation of long interspersed element-1 (L1, also known as LINE-1) transposons. A force of change in mammalian evolution, L1 elements are retrotransposons that have remained active during primate evolution. Decreased levels of L1-restricting factors APOBEC3B (also known as A3B) and PIWIL2 (ref. 7) in NHP iPS cells correlated with increased L1 mobility and endogenous L1 messenger RNA levels. Moreover, results from the manipulation of A3B and PIWIL2 levels in iPS cells supported a causal inverse relationship between levels of these proteins and L1 retrotransposition. Finally, we found increased copy numbers of species-specific L1 elements in the genome of chimpanzees compared to humans, supporting the idea that increased L1 mobility in NHPs is not limited to iPS cells in culture and may have also occurred in the germ line or embryonic cells developmentally upstream to germline specification during primate evolution. We propose that differences in L1 mobility may have differentially shaped the genomes of humans and NHPs and could have continuing adaptive significance. Humans, chimpanzees and bonobos are genetically very similar, sharing nearly 98% of their alignable genomic sequence. However, cellular and molecular phenotypes, especially at identical stages of development, are difficult to establish, mainly owing to limited access to embryonic material from humans and NHPs. We reprogrammed fibroblasts from two bonobos and two chimpanzees into iPS cells as previously described (Extended Data Fig. 1a). After culture in human embryonic stem (ES) cell-supporting conditions, NHP iPS cell colonies could be distinguished by the high nucleus-to-cytoplasm ratio morphology. iPS cell clones from both species continuously expressed pluripotency markers, retained an undifferentiated morphology in culture, and maintained a normal karyotype (Fig. 1a). After
CHROMOSOME COMPOSITION ANALYSIS OF VARIOUS SAC INTERSPECIFIC HYBRIDS BY GENOMIC IN SITU HYBRIDIS

Genomic in situ hybridisation (GISH) was used to analyse the chromosome composition of various interspecific Saccharum hybrids. In the nine cultivars studied, the proportion of complete S. spontaneum chromosomes ranged from 9% to 21%, and the proportion of chromosomes resulting from interspecific intrachromosomal exchanges ranged from 5% to 17%. There was no definite difference in the S. spontaneum contribution between the tropical and subtropicalltemperate clones tested. GISH showed that the three studied I1 interspecific hybrids between S. officinarum and S. spontaneum resulted from a 2n + n chromosome transmission typical of such crosses. The chromosome composition of 16 intergeneric hybrids between S. officinarum and E. arundinaceus was evaluated. Elimination of a few chromosolnes from one or both parental species was observed in all hybrids. In a clone classified as S. officinarum, which displayed 113 chromosomes instead of the typical 2n = 80 for this species, we found nine chromosomes derived from S. spontaneum, and four resulting from interspecific intrachromosomal exchanges between the two species. This suggests that clones with other than 80 chromosomes may not be pure S. officinarum. These results illustrate the potential of GISH for developing a better understanding of introgression processes and to better understand the complex genome structure of modern sugarcane varieties.
Functional Invariant Natural Killer T Cells Secreting Cytokines Are Associated With Non-Progressive Human Immunodeficiency Virus-1 Infection but Not With Suppressive Anti-Retroviral Treatment

Background CD1d restricted invariant natural killer T (iNKT) cells are important in the activation and regulation of immune responses. Limited information is available regarding the functional role of iNKT cells in the human immunodeficiency virus (HIV) disease progression. Methodology α-GalCer stimulated iNKT cells were characterized for their functionality in terms of cytokine production (IFN-γ, TNF-α, IL-2, IL-4, and IL-21) and CD107a expression in HIV-1 infected [23 long-term non progressors (LTNPs), 28 progressors, 18 patients before and after suppressive anti-retroviral treatment (ART)] along with 25 HIV-1 negative subjects using multicolor flow cytometry. Results The functional profile of α-GalCer stimulated iNKT cells was similar in LTNPs and healthy controls. The number of LTNPs showing functional response in terms of secretion of cytokines (IFN-γ/IL2/TNF-α) and CD107a expression was significantly higher than seen in the progressors. The cytokine secretion by the stimulated iNKT cells was predominantly Th1 type. The frequencies of iNKT cells showing secretion of IFN-γ or IL2 or TNF-α or expression of CD107a were higher in LTNPs (p < 0.05 for all) and also significantly associated with lower plasma viral load (p value ranged from 0.04 to 0.003) and higher CD4 count (p value ranged from 0.02 to <0.0001). The functional profile of the iNKT cells before and after ART did not differ significantly indicating absence of restoration of iNKT cells functionality after suppressive ART. The IL-4 and IL-21 secreting iNKT cells were rare in all study populations. Conclusion The presence of functional iNKT cells secreting number of cytokines in non-progressive HIV infection could be one of the multiple factors required to achieve HIV control and hence have relevance in understanding the immunity in HIV infection. The failure of restoration of the iNKT functionality after ART should be potential area of future research.
WHAT CAN A DATABASE OF PROTO-LANGUAGES TELL US ABOUT THE LAST 10 , 000 YEARS OF SOUND CHANGES ?

This paper describes the construction of a database on reconstructed phonological system and some of the preliminary interpretations. The statistical study of the content of over a hundred proto-phonological systems, does not reveal a significant evolution towards either complexification nor simplification, during the last 10,000 years. This means first that language reached a sufficient level of complexity long ago, and second that sound changes must not be viewed as teological processes, thus placing their motivations and explanations elsewhere. We also offer insights on some theoretical points raised by this study.
Turbulence effects on phytoplankton morphofunctional traits selection

Turbulence can regulate phytoplankton community structure in aquatic ecosystems by affecting sedimentation and nutrient acquisition. In rivers, nutrient concentrations are often high enough to sustain phytoplankton growth without limitation. Hence, turbulence mainly acts on phytoplankton by controlling its vertical position in such ecosystems. We conducted a laboratory experiment to see if the response of phytoplankton to turbulence could be predicted from morphofunctional traits related to sinking velocity and maximum growth rate. Turbulence was generated by horizontally oscillating grid systems in three 5 L chambers, which also constituted three chemostats. Two turbulence levels typical of lowland rivers (ɛ = 7.9 × 10−5 m2 s−3 and ɛ = 7.8 × 10−3 m2 s−3) were tested on an experimental community composed of six species from different taxonomic lineages. The species selected displayed different values for five morphofunctional traits related to sinking velocity and maximum growth rate (S : V ratio, algal unit size, density, shape, and motility). We showed that community structure could be partly predicted from morphofunctional traits. Under low turbulence (LT) (ɛ = 7.9 × 10−5 m2 s−3), species displaying traits leading to high sinking velocity (i.e., large size and high density) were unable to sustain stable populations, whereas species which displayed the opposite traits (i.e., small size, flattened shape, or low density) dominated the community. Furthermore, one of the six species exhibited phenotypic plasticity in size and could adapt to both high and LT conditions. © 2014 Association for the Sciences of Limnology and Oceanography
Bacterial leakage in implants with different implant-abutment connections: an in vitro study.

BACKGROUND Two-piece implants present gaps and cavities between the implant and the abutment, and these hollow spaces can act as a trap for bacteria. The aim of the present in vitro study was to evaluate the migration of two different microbial species from the inside to the outside of the implant-abutment assembly in three different connection types. METHODS A total of 30 implants (10 implants per group) were used. The implants presented a screwed trilobed connection (group 1), a cemented connection (group 2), and an internal conical connection (group 3). The inner parts of five implants, per group, were inoculated with Pseudomonas aeruginosa suspension and the remaining five implants, per group, with Aggregatibacter actinomycetemcomitans. The penetration of bacteria into the surrounding solution was determined by the observation of turbidity of the broth. RESULTS In group 1, bacterial contamination was found in six of 10 implants. In group 2, no contaminated samples were found. In group 3, bacterial contamination was found in one implant of 10. Statistically significant differences were detected between group 1 versus group 3 (P <0.05) and between group 1 versus group 2 (P <0.01), whereas no significant differences were found when comparing group 2 versus group 3 (P >0.05). CONCLUSION The present study confirms previous results about the hermeticity of the cement-retained implant-abutment assembly, the very low permeability to bacteria of the conical implant-abutment connection, and the high prevalence of bacterial penetration of screw-retained implant-abutment assemblies.
IFN-γ induces telomere attrition in aplastic anemia

Telomere attrition was reported in about 1/3 AA patients, but the precise pathogenesis is unclear. Our previously study found telomere length (TL) was closely related to patients’ immune status and the severity of disease condition. In this study we detected TL and IFN-γ of AA patients, we found a closely inverse relationship between serum IFN-γ level and TL of PWBC from AA. We followed up 4 AA patients who received ATG-based treatment and found that the recovery of IFN-γ level and telomere length was important for a good therapeutic response, poor prognosis and high clone transformation rate always couple with continuous high level of serum IFN-γ and extremely short telomere length (lower than 5 kb) for whatever reason. Cell experiment showed that both serum form SAA and IFN-γ could reduce the expression of hTERT of MOLT-4, which meant IFN-γ could induce telomere attrition by inhibiting telomerase activity. Our study suggested high level of IFN-γ may one of the most important causes that contributed to telomere attrition in AA patients.
Complex Relations in a Deep Structured Prediction Model for Fine Image Segmentation

Many deep learning architectures for semantic segmentation involve a Fully Convolutional Neural Network (FCN) followed by a Conditional Random Field (CRF) to carry out inference over an image. These models typically involve unary potentials based on local appearance features computed by FCNs, and binary potentials based on the displacement between pixels. We show that while current methods succeed in segmenting whole objects, they perform poorly in situations involving a large number of object parts. We therefore suggest incorporating into the inference algorithm additional higher-order potentials inspired by the way humans identify and localize parts. We incorporate two relations that were shown to be useful to human object identification - containment and attachment - into the energy term of the CRF and evaluate their performance on the Pascal VOC Parts dataset. Our experimental results show that the segmentation of fine parts is positively affected by the addition of these two relations, and that the segmentation of fine parts can be further influenced by complex structural features.
Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller

Three new potent neutralizing antibodies neutralize autologous HIV-1 strains and contribute to viral control in an HIV-1 controller. Antibodies can hold HIV-1 at an impasse Neutralizing antibodies put selective pressure on pathogens to mutate and escape from immune detection, which is one of the reasons why HIV-1 infection is difficult to contain. In this issue, Freund et al. studied samples spanning almost a decade from an individual who naturally controls HIV-1 infection without progressing to AIDS. They discovered three potent antibodies coexisting with viral strains that were sensitive to antibody neutralization, indicating that these antibodies may be contributing to viral control. These antibodies were also able to prevent HIV-1 viremia in humanized mice, demonstrating that the antibodies may be beneficial as passive immunotherapy for infected individuals. Some HIV-1–infected patients develop broad and potent HIV-1 neutralizing antibodies (bNAbs) that when passively transferred to mice or macaques can treat or prevent infection. However, bNAbs typically fail to neutralize coexisting autologous viruses due to antibody-mediated selection against sensitive viral strains. We describe an HIV-1 controller expressing HLA-B57*01 and HLA-B27*05 who maintained low viral loads for 30 years after infection and developed broad and potent serologic activity against HIV-1. Neutralization was attributed to three different bNAbs targeting nonoverlapping sites on the HIV-1 envelope trimer (Env). One of the three, BG18, an antibody directed against the glycan-V3 portion of Env, is the most potent member of this class reported to date and, as revealed by crystallography and electron microscopy, recognizes HIV-1 Env in a manner that is distinct from other bNAbs in this class. Single-genome sequencing of HIV-1 from serum samples obtained over a period of 9 years showed a diverse group of circulating viruses, 88.5% (31 of 35) of which remained sensitive to at least one of the temporally coincident autologous bNAbs and the individual’s serum. Thus, bNAb-sensitive strains of HIV-1 coexist with potent neutralizing antibodies that target the virus and may contribute to control in this individual. When administered as a mix, the three bNAbs controlled viremia in HIV-1YU2–infected humanized mice. Our finding suggests that combinations of bNAbs may contribute to control of HIV-1 infection.
Physical and Physiological Characteristics of an Elite Soccer Team’s Players According to Playing Positions

Abstract The purpose of this study was to evaluate and compare the positional physical and physiologicalcharacteristics of the elite soccer players based on anthropometric measurements, blood lactate, 5-10-20 m sprint,SJ, CMJ, Yo-Yo IR1 tests. For this purpose, measurements were taken from 29 professional soccer players (age:23.38±3.42) during the competitive season of 2013/14. The ANOVA one way with Tukey’s post hoc test was usedto determine the differences of the players at different playing positions. Wingers were the youngest, shortest,lightest, and had less BMI and fat percentange than the players at the other playing positions. The wingers were thefastest and midfielders were the slowest group in the team in 5m and 10m. Forwards showed the best performanceat SJ and CMJ in the team. The midfielders reached the highest and goalkeepers reached the lowest velocity at 2,2.5, 3 and 4 mmol blood lactate levels. The wingers reached the best and the goalkeepers were/had the lowestdistance at Yo-Yo IR1. Full backs reached a better distance than the midfielders, forwards and center backsrespectively. The results clearly indicated that there are physical and physiological differences according to theplaying position of soccer players.
EFFECT OF THREE DIFFERENT EXTENDERS IN SLOW FREEZING PROTOCOL ON POST-THAW QUALITY OF DOG SEMEN*

Forty dog semen ejaculates were diluted in three extenders at the rate of 1:3, and subjected to slow freezing in a programmable freezer. Tris and Triladyl extenders were superior and significantly different from Laiciphos-488 (p< 0.01) on postthaw values for motility, live sperm and membrane integrity in slow freezing protocol.
Q uality evaluation of acetaminophen formulations manufactured in Congo DR

The objective of this work was to study t he acce lerated stability of Acetaminophen 500mg tablet sold on the Congolese market. Five specialties of Acetaminophen were examined: four locally manufactured generics and the innovator. Two analytical tests were made to study the change during the storage: The dosage of active ingredient by HPLC and dissolution profile by UV / Visible spectrophotometer. The results of this study reveal a problem with the manufacturing processes of Congolese generics. That is caused because they all present an abnormal drop of active ingredient and a release below the limit, from the sixth month of storage at a temperature and relative humidity of 40 °C and 75%. HR as per ICH guidelines .
Lozenge Tilings of a Halved Hexagon with an Array of Triangles Removed from the Boundary

Proctor's work on staircase plane partitions yields an enumeration of lozenge tilings of a halved hexagon on the triangular lattice. Rohatgi later extended this tiling enumeration to a halved hexagon with a triangle cut off from the boundary. In the previous paper, the author proved a common generalization of Proctor's and Rohatgi's results by enumerating lozenge tilings of a halved hexagon in the case an array of an arbitrary number of triangles has been removed from a non-staircase side. In this paper, we consider the other case when the array of triangles has been removed from the staircase side of the halved hexagon. Our result also implies an explicit formula for the number of tilings of a hexagon with an array of triangles missing on the symmetry axis.
Synchrosqueezing-based Transform and its Application in Seismic Data Analysis

Seismic waves are non-stationary due to its propagation through the earth. Time-frequency transforms are suitable tools for analyzing non-stationary seismic signals. Spectral decomposition can reveal the non-stationary characteristics which cannot be easily observed in the time or frequency representation alone. Various types of spectral decomposition methods have been introduced by some researchers. Conventional spectral decompositions have some restrictions such as Heisenberg uncertainty principle and cross-terms which limit their applications in signal analysis. In this paper, synchrosqueezingbased transforms were used to overcome the mentioned restrictions; also, as an application of this new high resolution time-frequency analysis method, it was applied to random noise removal and the detection of low-frequency shadows in seismic data. The efficiency of this method is evaluated by applying it to both synthetic and real seismic data. The results show that the mentioned transform is a proper tool for seismic data processing and interpretation.
Fair Division and Generalizations of Sperner- and KKM-type Results

We treat problems of fair division, their various interconnections, and their relations to Sperner's lemma and the Knaster--Kuratowski--Mazurkiewicz (KKM) theorem as well as their variants. We prove extensions of Alon's necklace splitting result in certain regimes and relate it to hyperplane mass partitions. We show the existence of fair cake division and rental harmony in the sense of Su even in the absence of full information. Furthermore, we extend Sperner's lemma and the KKM theorem to (colorful) quantitative versions for polytopes and pseudomanifolds. For simplicial polytopes our results turn out to be improvements over the earlier work of De Loera, Peterson, and Su on a polytopal version of Sperner's lemma. Moreover, our results extend the work of Musin on quantitative Sperner-type results for piecewise linear manifolds.
PieAPP: Perceptual Image-Error Assessment Through Pairwise Preference

The ability to estimate the perceptual error between images is an important problem in computer vision with many applications. Although it has been studied extensively, however, no method currently exists that can robustly predict visual differences like humans. Some previous approaches used hand-coded models, but they fail to model the complexity of the human visual system. Others used machine learning to train models on human-labeled datasets, but creating large, high-quality datasets is difficult because people are unable to assign consistent error labels to distorted images. In this paper, we present a new learning-based method that is the first to predict perceptual image error like human observers. Since it is much easier for people to compare two given images and identify the one more similar to a reference than to assign quality scores to each, we propose a new, large-scale dataset labeled with the probability that humans will prefer one image over another. We then train a deep-learning model using a novel, pairwise-learning framework to predict the preference of one distorted image over the other. Our key observation is that our trained network can then be used separately with only one distorted image and a reference to predict its perceptual error, without ever being trained on explicit human perceptual-error labels. The perceptual error estimated by our new metric, PieAPP, is well-correlated with human opinion. Furthermore, it significantly outperforms existing algorithms, beating the state-of-the-art by almost 3Ã— on our test set in terms of binary error rate, while also generalizing to new kinds of distortions, unlike previous learning-based methods.
Development of a Discriminative Intrinsic Dissolution Method for Efavirenz

Efavirenz is a poorly water-soluble drug categorized as a Class 2 drug under the Biopharmaceutics Classification System (BCS). Intrinsic dissolution is an effective tool for evaluating the physical–chemical properties of an active pharmaceutical ingredient (API). The aim of this study was to develop an intrinsic dissolution method for use in quality control of efavirenz to be used in the selection of an API for the production of dosage forms. The influence of compression force, rotation speed, dissolution medium, and surfactant concentration on the intrinsic dissolution rate (IDR) of efavirenz were evaluated using a rotating-disk holder. The developed method was applied to the evaluation of batches using different raw materials (batches A–G). Dissolution media containing 0.5% sodium lauryl sulfate (SLS) and a rotation speed of 100 rpm proved the most discriminative. Batches A, D, and F provided intrinsic dissolution rate (IDR) values greater than 36 μg/min/cm2 in this medium, while batches B and E provided IDR values of approximately 31 μg/min/cm2. The IDRs obtained showed a high correlation with the surface areas of the batches. The method may be used in the development of efavirenz formulations to select API with physical–chemical properties that enable appropriate dosage form dissolution.