Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of Alternative Functions of the Mitochondrial Protein Bak

2 Nontechnical Abstract . 3 Objective . 4 Introduction . 5 Mitochondria and Apoptosis . 5 MAC formation . 5 Molecular structures of Bax and Bak . 6 Mitochondrial ROS production . 8 Materials and Methods . 11 Culturing and maintaining of mammalian cell lines . 11 Isolation of intact mitochondria . 12 Live-Cell imaging of mitochondrial ROS emission by fluorescence microscopy . 14 Spectrofluorimetric measurement of ROS emission from mitochondria . 15 Results and Discussion . 17 Closing Remarks . 24 References . 25 Glossary . 26 Honor Thesis: Study of Alternative Functions of the Mitochondrial Protein Bak 2
Stance Detection for the Fake News Challenge

Fake News is a real problem nowadays with the advent of social media and the lack of knowledge among the average populace. Fact checking can be a long and drawn out process and not every person has the time to verify the sources of every news article they come across. In such a scenario, our best bet is to develop and perfect the techniques in the areas of Artificial Intelligence and Natural Language Processing. For the purpose of this project, we will be focusing on “Stance Detection” stage of the identifying “Fake News” articles. The problem is quite well-defined, and a considerable amount of work has been done in this area. The input would be a corpus of headline-article pairs and the output will be the classification of the articles on the basis of whether their headline and content agree, disagree, discuss, or are unrelated. Our team focused on using different models for the above-mentioned task and compare the results to the baseline method provided by the organizers of Fake News challenge. This report summarizes our approaches, experiments, and results and we also discuss what are the state-of-the-art techniques for this task.
Numerical simulation of microchannel network with complex geometry

The paper presents the results of a numerical study devoted to the hydraulic properties of a network of parallel triangular microchannels (hydraulic diameter Dh = 110 μm). Previous experimental investigations had revealed that pressure drop through the microchannels system dramatically increases for the Reynolds number exceeding value of 10. The disagreement of the experimental findings with the estimations of flow resistance based on the assumption of fully developed flow were suspected to result from the so-called scale effect. Numerical simulations were performed by using the classical system of flow equations (continuity and Navier-Stokes equations) in order to explain the observed discrepancies. The calculations showed a very good agreement with the experimental results proving that there is no scale effect for the microchannels considered, i.e. the relevance of the constitutive flow model applied was confirmed. It was also clearly indicated that the excessive pressure losses in the high Reynolds number range are due to the secondary flows and separations appearing in several regions of the microchannel system.
Green Composites from Ionic Liquid-Assisted Processing of Sustainable Resources: A Brief Overview

The massive use of synthetic, petroleum-based polymeric composites has disturbed the fragile environmental equilibrium of our planet. Composites made solely from polysaccharides can offer unique intrinsic properties such as renewability, biodegrad- ability, easy availability, eco-friendliness, facile processing, flexibility, and exciting physico-mechanical characteristics. The development of green processing of lignocel- lulosic materials and bio-based polymers such as cellulose, starch, chitin, and chitosan, the most abundant biorenewable materials on earth, is urgent from the perspectives of both environmental protection and sustainability in materials industries. Recently, the enormous potential of ionic liquids (ILs) as an alternative to ecologically harmful conventional organic solvents has been well recognized. Presently, a wide range of pronounced approaches have been explored to further improve the performance of ionic liquid-based processing of polysaccharides for green composite manufacturing. This review presents recent technological developments in which the advantages of ionic liquids as a dissolution medium for polysaccharides for production of plethora of green composites have been gradually realized.
Are Tonsils and Adenoids Secondary Reservoirs for Helicobacter pylori in Children? Why it Matters!!

The study aimed at demonstration of the possible existence of Helicobacter pylori in tonsils and adenoids and its possible risk sequences. The stomach wall represents the main and commonest habitat for H. pylori since an immemorial time; in a way indicating that mucosa of the stomach is the structure of the body that can recognize that stomach bacterium. Therefore; migration of H. pylori outside the stomach could encode autoimmunity. Tonsils and adenoids are lately discovered as secondary reservoirs for H. pylori in children. Further reports have confirmed the association of adenotonsillar hypertrophy with cytotoxin-associated gene A (cagA) positive H. pylori strains, and emphasized that cagA of H. pylori encodes high immunogenicity. Migration of H. pylori into the circulation could be an open gate for systemic complications; although H. pylori bacteremia is not a recognized behavior of a bacterium used to colonize the stomach, yet H. pylori bacteremia is clearly reported in literature. H. pylori can reside in dental plaques where it can feed on remnants of food in the mouth or bleeding from gums. Therefore; surgery on hypertrophied tonsils while migrating H. pylori strains exist around could attract these strains to gain feeding on the resulting oozing tonsil’s surgical bed with the possible potential risk and sequels of H. pylori bacteremia. 30 children aged 10-12 years with frank symptoms and family history of H. pylori dyspepsia scheduled for surgery because of hypertrophy of tonsils and adenoids were included in the study. They were divided into three equal groups; group 1 followed natural H. pylori eradication therapy and group 2 underwent surgery while group 3 followed antibiotic therapies before surgery. Existence of H. pylori strains was proved in children and parents by specific tests (urea breath test and H. pylori fecal antigen test). All children and parents were found positive for colonic H. pylori strains. Urea breath test was positive in most children. Adenoid/tonsil surgical specimens were mostly positive for H. pylori DNA. Regression of hypertrophy of tonsils was demonstrated in most children of the natural therapy first group and 7 of 10 children escaped surgery. On conclusion, existence of H. pylori should be ruled out and eliminated from the throat by natural measures before surgery of hypertrophied tonsils demonstrating no suppuration or inflammation.
Using passive and active enumeration methods to improve IPv 6 host enumeration search algorithms

IPv6 off-link host enumeration, when compared to IPv4 host enumeration, is a difficult and expensive exercise. The expense arises from the difference in address space sizes between the two protocols, with IPv6 having a 2 96 larger address space than that of IPv4. This paper presents an algorithm for performing contextual IPv6 host enumeration against a target. The algorithm uses passive and active enumeration in order to focus the search upon areas of the address space where it is more probable that targets will exist. Experiments were conducted to test the proposed adaptive heuristic search algorithm involving applying the algorithm to a test dataset of IPv6 addresses, measuring the results and comparing those to a linear search against the same datasets. This research shows that the adaptive heuristic search algorithm achieved an average of 9,975 successful hits per simulation when applied to a dataset of realistic IPv6 addresses, whilst the linear search had an average of 8,642 when applied to the same dataset. Both algorithms performed poorly when applied to a dataset comprising randomly generated IPv6 addresses. The results show that the algorithm provides a good candidate for IPv6 off-link host enumeration, as it outperformed the linear search on average, whilst using less probes to do so.
mutations in melanoma patients with additional cancer and cancer in their family history

Germline mutations of the tumour suppressor gene CDKN2A/p16 have been reported in association CDKN2A/p16 have been reported in association CDKN2A/p16 with familial melanoma, sporadic melanoma and pancreatic cancer. We studied the possibility of mutations in the CDKN2A/p16 gene in patients with melanoma and additional unrelated cancer and CDKN2A/p16 gene in patients with melanoma and additional unrelated cancer and CDKN2A/p16 in patients with additional unrelated cancer in their family history as well. Twenty fi ve melanoma patients with additional cancer and twenty six melanoma patients with additional unrelated cancer in their family history were studied. The entire coding region of the CDKN2A/p16 gene was screened CDKN2A/p16 gene was screened CDKN2A/p16 by single stranded conformation polymorphism analyses and direct DNA sequencing. No germline mutations were detected in the observed melanoma patients. The previously described Ala148Thr and 500 C/G polymorphism were detected. It appears that the cancer development in the patients studied is related to a combination of low-risk susceptibility genes and environmental factors.
Front-Door Versus Back-Door Adjustment With Unmeasured Confounding: Bias Formulas for Front-Door and Hybrid Adjustments With Application to a Job Training Program

ABSTRACT We demonstrate that the front-door adjustment can be a useful alternative to standard covariate adjustments (i.e., back-door adjustments), even when the assumptions required for the front-door approach do not hold. We do this by providing asymptotic bias formulas for the front-door approach that can be compared directly to bias formulas for the back-door approach. In some cases, this allows the tightening of bounds on treatment effects. We also show that under one-sided noncompliance, the front-door approach does not rely on the use of control units. This finding has implications for the design of studies when treatment cannot be withheld from individuals (perhaps for ethical reasons). We illustrate these points with an application to the National Job Training Partnership Act Study.
Data Dispersion: Now You See It… Now You Don't

Poisson regression is the most well-known method for modeling count data. When data display over-dispersion, thereby violating the underlying equi-dispersion assumption of Poisson regression, the common solution is to use negative-binomial regression. We show, however, that count data that appear to be equi- or over-dispersed may actually stem from a mixture of populations with different dispersion levels. To detect and model such a mixture, we introduce a generalization of the Conway-Maxwell-Poisson (COM-Poisson) regression model that allows for group-level dispersion. We illustrate mixed dispersion effects and the proposed methodology via semi-authentic data.
Effect of Krill Oil Application on Wound Healing in Male Rats

Wound healing is an active process of communication between cells, matrix, and various growth factors. Krill oil is a rarely used substance having medicinal properties with wound healing, as anti-inflammatory, antioxidant and renewal of tissues. The current study aimed to study the role of krill oil in the wounded skin healing and repair. Skin wound incisions were performed in the right thigh area of thirty mature male rats (aged 10 weeks and weighing 165±4.5 g). Wounded skin rats were assigned into two equal groups. Wounded areas were daily treated with a local application of 1 μL of normal saline (control group) and 1 μL of krill oil (treatment group). After 1, 5, and 10 days, five rats from each group were sacrificed and tissue samples from the wounded areas were obtained for histopathological examination. Histopathological examination revealed time-dependent successive acceleration of wound healing in the krill oil-treated rats compared with that of control rats throughout the experimental period. Improvements were observed with regard to the level of epithelialization, infiltration of inflammatory cells, and constriction of the wound area. In conclusion, local application of krill oil has therapeutic efficiency to accelerate wound healing.
Financial Market Reaction to Federal Reserve Communications: Does the Crisis Make a Difference?

This paper studies the effects of Federal Reserve communications on US financial market returns from 1998 to 2009 and asks whether a significant change occurred during the financial crisis of August 2007–December 2009. We find, first, that central bank communication moves financial markets in the intended direction. In particular, shorter maturities are affected in an economically meaningful way. Second, speeches by the Chairman generate relatively more public attention than communication by other governors or presidents. Finally, central bank communication is even more market relevant during the financial crisis subsample.
Temporal variation in coral reef ecosystem processes: herbivory of macroalgae by fishes

Despite the widely accepted importance of fish herbivory on coral reefs, few studies have considered the temporal variability in the nature of algal–herbivore interactions. We therefore quantified monthly feeding intensity on Sargassum sp. bioassays for 12 mo with remote underwater video cameras deployed to identify the herbivores responsible for macroalgal removal on an inshore island of the Great Barrier Reef, Australia. Significantly higher removal rates were observed during the summer months whereas winter months were characterized by 4 times lower removal rates. However, rather than being simply changes in the feeding activity of a single species, this temporal pattern in herbivory also incorporated changes in the species responsible for the removal of Sargassum. Video analyses revealed that, of the 43 herbivore species recorded from the bay, only 3 played a significant role in Sargassum removal: Kyphosus vaigiensis, Naso unicornis and Scarus rivulatus. K. vaigiensis, a rudderfish, was primarily responsible for the removal of Sargassum during the summer months (83% of the total recorded bites; 85553 bites). There was almost no feeding activity on Sargassum by K. vaigiensis during the winter months (82 bites). However, there was a reciprocal increase in feeding intensity on Sargassum by parrotfishes in the winter months, particularly S. rivulatus (71 bites during summer versus 2884 bites in winter). This temporal variability in herbivore functional roles suggests that functional redundancy on reefs may be less than previously assumed in that the feeding activities of fishes may be both spatially and temporally constrained.
An updated discussion of the solar abundance problem

We discuss the level of agreement of a new generation of standard solar models (SSMs), Barcelona 2016 or B16 for short, with helioseismic and solar neutrino data, confirming that models implementing the AGSS09met surface abundances, based on refined three-dimensional hydrodynamical simulations of the solar atmosphere, do not not reproduce helioseismic constraints. We clarify that this solar abundance problem can be equally solved by a change of the composition and/or of the opacity of the solar plasma, since effects produced by variations of metal abundances are equivalent to those produced by suitable modifications of the solar opacity profile. We discuss the importance of neutrinos produced in the CNO cycle for removing the composition-opacity degeneracy and the perspectives for their future detection.
Sugarcane bagasse derived nano magnetic adsorbent composite (SCB-NMAC) for removal of Cu2+ from aqueous solution

A novel sugarcane bagasse derived nano magnetic adsorbent composite (SCB-NMAC) was successfully prepared for the removal of Cu2+ in aqueous solution. Characterization of the newly prepared material was obtained through SEM, EDX, particle size analyzer and XRD. Results confirmed the presence of iron oxide coating onto the material. The removal of Cu2+ by SCB-NMAC obeyed the pseudo second order reaction (R2 = 0.982) as opposed to intra particle diffusion (R2 = 0.708), and pseudo first order (R2 = 0.402) model. Langmuir isotherm was found to be more applicable (R2 = 0.996) rather than Freundlich isotherm (R2 = 0.979), which indicated a monolayer adsorption between Cu2+ and SCB-NMAC. The maximum adsorption capacity was calculated as 113.63 mg/g at pH 4. In addition, adsorption-desorption studies indicated that SCB-NMAC displayed high stability for regeneration with good reusability with desorption efficiency up to 60% and reusability efficiency up to 80% for three recurring cycles.
Development of connected permeability in massive crystalline rocks through hydraulic fracture propagation and shearing accompanying fluid injection

The ability to generate deep flow in massive crystalline rocks is governed by the interconnectivity of the fracture network and its permeability, which in turn is largely dependent on the in situ stress field. The increase of stress with depth reduces fracture aperture, leading to a decrease in rock mass permeability. The frequency of natural fractures also decreases with depth, resulting in less connectivity. The permeability of crystalline rocks is typically reduced to about 10 � 17 –10 � 15 m 2 at targeted depths for enhanced geothermal systems (EGS) applications, that is, >3 km. Therefore, fluid injection methods are required to hydraulically fracture the rock and increase its permeability. In the mining sector, fluid injection methods are being investigated to increase rock fragmentation and mitigate high-stress hazards due to operations moving to unprecedented depths. Here as well, detailed understanding of permeability and its enhancement is required. This paper reports findings from a series of hydromechanically coupled distinct-element models developed in support of a hydraulic fracture experiment testing hypotheses related to enhanced permeability, increased fragmentation, and modified stress fields. Two principal injection designs are tested as follows: injection of a high flow rate through a narrow-packed interval and injection of a low flow rate across a wider packed interval. Results show that the development of connected permeability is almost exclusively orthogonal to the minimum principal stress, leading to strongly anisotropic flow. This is because of the stress transfer associated with opening of tensile fractures, which increases the confining stress acting across neighboring natural fractures. This limits the hydraulic response of fractures and the capacity to create symmetric isotropic permeability relative to the injection wellbore. These findings suggest that the development of permeability at depth can be improved by targeting a set of fluid injections through smaller packed intervals instead of a single longer injection in open boreholes.
Seismic imaging of deep low‐velocity zone beneath the Dead Sea basin and transform fault: Implications for strain localization and crustal rigidity

New seismic observations from the Dead Sea basin (DSB), a large pull‐apart basin along the Dead Sea transform (DST) plate boundary, show a low velocity zone extending to a depth of 18 km under the basin. The lower crust and Moho are not perturbed. These observations are incompatible with the current view of mid‐crustal strength at low temperatures and with support of the basin's negative load by a rigid elastic plate. Strain softening in the middle crust is invoked to explain the isostatic compensation and the rapid subsidence of the basin during the Pleistocene. Whether the deformation is influenced by the presence of fluids and by a long history of seismic activity on the DST, and what the exact softening mechanism is, remain open questions. The uplift surrounding the DST also appears to be an upper crustal phenomenon but its relationship to a mid‐crustal strength minimum is less clear. The shear deformation associated with the transform plate boundary motion appears, on the other hand, to cut throughout the entire crust.
Schottky barrier heights at polar metal/semiconductor interfaces

Using a first-principle pseudopotential approach, we have investigated the Schottky barrier heights of abrupt Al/Ge, Al/GaAs, Al/AlAs, and Al/ZnSe (100) junctions, and their dependence on the semiconductor chemical composition and surface termination. A model based on linear-response theory is developed, which provides a simple, yet accurate description of the barrier-height variations with the chemical composition of the semiconductor. The larger barrier values found for the anion-terminated surface than for the cation-terminated surface are explained in terms of the screened charge of the polar semiconductor surface and its image charge at the metal surface. Atomic-scale computations show how the classical image charge concept, valid for charges placed at large distances from the metal, extends to distances shorter than the decay length of the metal-induced-gap states.
A triage approach to improve the relevance of marine ecosystem services assessments

Ecosystem services assessments are increasingly being used to inform marine policy and planning. These assessments involve significant time, effort, and expertise. It is important at the outset to determine which of many ecosystem services should be quantified and which meas- ures of ecological output, economic impact, or value should be assessed. Furthermore, the litera- ture shows that in practice such assessments are unevenly applied and rarely used effectively in decision-making processes. We develop a structured decision-making approach, called a triage, to assess what types of ecosystem services should be assessed to improve the uptake and useful- ness of such information in marine planning. Two case studies, in France and the United Kingdom, provide examples of the application of the triage approach.
AVATS : Awake Video Assisted Thoracic Surgery in Complex Thoracic Procedures

Background: Traditionally, video-assisted thoracic surgery (VATS) is performed under general anesthesia with selective ventilation and endotracheal intubation. In 2014, we published our experience with awake VATS performed under local anesthesia (AVATS) extending the benefits of VATS to those unable to tolerate general anesthesia and improve outcomes. Method: Currently we reviewed a total of 494 AVATS procedures from June 2010 to January 2016, having added 201 new cases performed with AVATS to our original series. We have extended this technique to include more complex procedures, with results that surpass traditional open thoracotomies and traditional VATS under general anesthesia. Results: Procedures such as pleural biopsies, wedge resections, decortications, pleurodesis, lobectomies, bullectomies and pericardial windows were previously reported with the AVATS technique in our original paper. We have analyzed our additional volume of these procedures using AVATS and have extended the AVATS technique to repair of esophageal perforations, bronchopleural fistulae, diaphragmatic laceration and chyle leak. Conclusion: With proper patient selection and careful preoperative planning AVATS may be safely used to perform even complex thoracic surgery with equal or improved outcomes without compromise in safety.