Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Tumor Progression by the Sequential Introduction of Genetic Alterations into the Genome of Human Normal Cells

Cancer genomes display a complex blend of genetic lesions affecting oncogenes and tumor suppressor genes. Multiple modeling approaches indicate that 5–15 driver oncogenic events are required to achieve tumor progression in common epithelial cancers. In vitro, a lower number (2–3) of events is typically sufficient to achieve full transformation. We developed cellular models that closely resemble the occurrence of multiple genetic lesions to understand their role in tumor progression. Homologous recombination and transcriptional downregulation were used to recapitulate the co‐occurrence of driver mutations targeting oncogenes and inactivation of tumor suppressor genes in human nontransformed epithelial cells. Knockdown of the tumor suppressor genes PTEN or RB1 was combined with mutagenic activation of individual oncogenes (EGFR, KRAS, BRAF, or PIK3CA), thus generating a combinatorial model. The simultaneous presence of oncogenic and tumor suppressive events resulted in distinct biochemical properties and anchorage‐independent growth abilities. Notably, however, we found that even when up to four individual alterations were concomitantly present they were not sufficient to fully transform the target cells. Our results suggest that the close recapitulation of cancer lesions in not‐transformed cells is essential to unveil their oncogenic potential and raise questions concerning the minimal requirements for neoplastic transformation of epithelial cells.
Watermarking 3D models

Copyright protection of graphical objects and models is important for protecting author rights in animation, multimedia, computer-aided design (CAD), virtual reality, medical imaging, etc. We suggest a blind watermarking algorithm for 3D models and objects. A string of bits, generated according to a key, is embedded in the geometrical structure of the graphical object by changing the locations of certain vertices. The criterion to choose these vertices ensures a minimal visibility of the distortions in the watermarked object. A bit encoding 1 is associated with positioning a vertex inside a volume modelled by the geometry of its neighbourhood, while a bit encoding 0 positions the vertex outside such a volume. The proposed watermarking algorithm is applied on various 3D models.
Lactation and bone turnover: a conundrum of marked bone loss in the setting of coupled bone turnover.

CONTEXT Mothers who exclusively breastfeed lose up to 10% of their bone mass. This is primarily mediated by PTHrP, in combination with low estrogen levels. The mechanisms underlying this marked bone loss are unknown. Uncoupling of bone turnover, which is seen in other prototypical states of bone loss, would seem the likely explanation. However, the most current markers of bone turnover have not been studied in human lactation. OBJECTIVES The purpose of this study was to assess bone formation in lactating humans using the most current bone turnover markers. DESIGN AND PARTICIPANTS We conducted a prospective cohort study with repeated measures of bone metabolism in a volunteer sample of 49 women, recruited into three study groups: lactating, bottle feeding, and healthy controls. The postpartum women were studied at 6-8 and 12-14 wk postpartum, whereas the controls were studied at the follicular phase of their menstrual cycles. OUTCOME MEASURES Biochemical markers of bone turnover were assessed. RESULTS Mean serum C-telopeptide of type I collagen, a sensitive marker of bone resorption, was approximately 2-fold higher in lactating women as compared with bottle-feeding and healthy controls (P = 0.037 and P < 0.001, respectively). Surprisingly, amino-terminal telopeptides of procollagen 1, the most current marker of bone formation, bone-specific alkaline phosphatase, and osteocalcin were all significantly higher in the lactating group as compared with controls (P < 0.001, P = 0.002, and P < 0.001, respectively). CONCLUSIONS In contrast to prototypical states of rapid bone loss (myeloma, cancer, and immobilization) in which markers of bone turnover display marked uncoupling, lactational bone loss, as assessed in this small exploratory study, is distinct, showing comparably rapid bone loss in the face of apparent osteoclast-osteoblast coupling.
The use of icons and labels in an end user application program: An empirical study of learning and retention

This research compared the learning of an application program whose interface was implemented using buttons with text labels, icons, or a fully redundant combination of icons and text labels. The objective was to: 1) evaluate the success of novice computer users in initially learning to use the application and in later use in a delayed session and 2) measure users' attitudes toward the application. Each session was divided into four blocks, and performance in the blocks was measured in terms of correctness of the tasks performed, time to perform tasks, and number of times the help facility was accessed. In addition, at the end of each session the participants' perceptions of the ease of use and usefulness of the software were measured. The results showed that in the first session performance was best on the label-only and icon-label interfaces. Performance on the icon-only interface was much poorer in session 1, particularly in terms of time and help references, but improved in session 2 to the point wher.
Why Amantadine Loses Its Function in Influenza M2 Mutants: MD Simulations

Molecular dynamics simulations of the drug-resistant M2 mutants, A30T, S31N, and L26I, were carried out to investigate the inhibition of M2 activity using amantadine (AMT). The closed and open channel conformations were examined via non- and triply protonated H37. For the nonprotonated state, these mutants exhibited zero water density in the conducting region, and AMT was still bound to the channel pore. Thus, water transport is totally suppressed, similar to the wild-type channel. In contrast, the triply protonated states of the mutants exhibited a different water density and AMT position. A30T and L26I both have a greater water density compared to the wild-type M2, while for the A30T system, AMT is no longer inside the pore. Hydrogen bonding between AMT and H37 crucial for the bioactivity is entirely lost in the open conformation. The elimination of this important interaction of these mutations is responsible for the lost of AMT's function in influenza A M2. This is different for the S31N mutant in which AMT was observed to locate at the pore opening region and bond with V27 instead of S31.
Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism

Gravitropic bending of plant organs is mediated by an asymmetric signaling of the plant hormone auxin between the upper and lower side of the respective organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows asymmetric action during gravitropic responses. Immunodetection using an antibody against GA and monitoring GA signaling output by downstream degradation of DELLA proteins revealed an asymmetric GA distribution and response with the maximum at the lower side of gravistimulated roots. Genetic or pharmacological manipulation of GA levels or response affects gravity-mediated auxin redistribution and root bending response. The higher GA levels at the lower side of the root correlate with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane. The observed increase in PIN2 stability is caused by a specific GA effect on trafficking of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin A-sensitive endosomes. Our results suggest that asymmetric auxin distribution instructive for gravity-induced differential growth is consolidated by the asymmetric action of GA that stabilizes the PIN-dependent auxin stream along the lower side of gravistimulated roots.
Safety of Non-Vitamin K Antagonist Oral Anticoagulants in Clinical Practice: Focus on Rivaroxaban in Stroke Prevention in Patients With Atrial Fibrillation

Despite direct oral anticoagulants (DOACs) have overcome the most relevant limitations of vitamin K antagonists, many patients with atrial fibrillation are not receiving the appropriate anticoagulant therapy. In addition, when patients are anticoagulated with DOACs, some of them are not taking the dose recommended in the summary of product characteristics. This may be related, at least in part, to the concern about the applicability of findings from randomized clinical trials to real-life patients. In this context, performing studies in daily clinical practice to assess the efficacy and safety of DOACs in real-world setting is mandatory. The aim of this review is to update the current evidence regarding safety of rivaroxaban in clinical practice. The Rivaroxaban Once Daily Oral Direct Factor Xa Inhibition Compared with Vitamin K Antagonism for Prevention of Stroke and Embolism Trial in Atrial Fibrillation (ROCKET-AF) showed that rivaroxaban was at least as effective as warfarin for preventing stroke or systemic embolism, with similar rates of major bleeding but with lesser risk of intracranial and fatal bleedings. Data from noninterventional studies and registries have confirmed the good results of ROCKET-AF. Even more, rates of bleeding may be inferior in real-life patients, since they have a lower risk profile than those included in ROCKET-AF.
Simulation of the contact between a rough surface and a viscoelastic material with friction

Tires are a key component for the handling and safety of personal vehicles. In this thesis a model of the contact between the tire tread and a dry road is described. It aims at understanding the different physical phenomena taking place in such a contact and their relative role in tire friction. Modeling the multiple scales of road roughness is difficult using a standard Finite Element Method. The hypothesis that the rubber of the tire tread is very large compared to the largest scale of surface roughness is made, so that it can be considered as a semi-infinite half-space. This way, the contact problem can be solved by discretizing the rubber surface only. The solver is a specific Conjugate Gradient iterative method, in which the matrix-vector products are performed with Fast Fourier Transforms. Transient viscoelasticity is accounted for with a step-by-step approach. The algorithm is able to model surface interactions such as Coulomb friction and adhesion. Results show the crucial role played by viscoelasticity. Coupled with the road roughness, it changes the contact surface during the different steps of tire sliding, which in turns impacts friction.
Abs-Laplacian and Robert ’ s cross operator offers high speed edge detection capabilities with comparable speed-quality tradeoffs

Abs-Laplacian is a newer technique for detecting edges. While the Sobel and Prewitt seems to be used predominantly in image processing due to better edge detection. However they need higher amount of complexity twice than that of abs-Laplacin. Moreover, qualities of images are no better than the newer kernel. While the new technique seems to perform better in speed and quality, there seems a bit of competition with the 1 order kernel i.e. Robert’s cross operator. In terms of speed, Robert needs only 3 computational units against 7 for abs-Laplacian, but in terms of image quality analyzed by determining the intensity deviation of Robert’s edge or abs-Laplacian edges with respect to the Sobel’s edges shows that Robert’s kernel show major deviation indicating a low quality image while the new technique showed negligible deviation. Intensity profiles of edges detected for various kinds of images shows similar behavior for each kernel which also suggests that the inherent nature of kernels tend to remain the same for whatever complex images we deal with. In conclusion, the results show that there exists a speedquality tradeoff between the abs-Laplacian and the Roberts operators.
The Linked Data Mining Challenge 2014: Results and Experiences

The 2014 edition of the Linked Data Mining Challenge, con- ducted in conjunction with Know@LOD 2014, has been the third edi- tion of this challenge. The underlying data came from two domains: public procurement, and researcher collaboration. Like in the previous year, when the challenge was held at the Data Mining on Linked Data workshop co-located with the European Conference on Machine Learn- ing and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2013), the response to the challenge appeared lower than expected, with only one solution submitted for the predictive task this year. We have tried to track the reasons for the continuously low partic- ipation in the challenge via a questionnaire survey, and principles have been distilled that could help organizers of future similar challenges.
Inhibition of Apoptosis in Periodontitis

This study investigated whether the prolonged survival of inflammatory cells in periodontal disease could be due to the inhibition of apoptosis by tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) decoy receptors and inhibition of the terminal stages of apoptosis signaling by inhibitor of apoptosis (IAP) family members. Gingival tissue samples were taken from healthy individuals and those with chronic periodontitis. The expression of TRAIL, TRAIL receptors, TUNEL, cleaved caspase-3, xIAP, and survivin was determined immunohistologically and at the level of mRNA expression. Higher levels of TRAIL and the TRAIL decoy receptor, TRAIL R4, were expressed in the diseased periodontal tissues (p < 0.005). Statistically (p < 0.05) higher levels of cleaved caspase-3 and the cleaved caspase-3 inhibitors, xIAP and survivin, were seen. Similar changes were seen at the level of mRNA. The results indicate that apoptosis in periodontitis may be inhibited by elevated expression of TRAIL decoy receptors and cleaved caspase-3 inhibitors.
Polyamide Nanofibers Reinforced Titanium Nanoparticles Composites for hydrophobic surfaces

In this study, samples of polyamide (6) (PA 6) nanofibers armed with TiO2 nanoparticles were prepared using an electrospinning method for the preparation of nanocomposite fibres. The nanofibers were prepared under 0.15% weight, 25 kV applied voltage, 15 cm electrospinning distance, 0.48 mm tip diameter and 0.3 ml/hr injection rate to obtain nanofibers with a diameter of about 100 nm and then reinforced with (50 nm diameter ) Titanium Nanoparticles. The properties and morphology of the surface were studied using the atomic force microscopy (AFM) scanner. The polyamide structure was also examined by the Fourier transform infrared radiation (FTIR) infrared device, and the contact angle was measured with water using a contact angle analyzer. The results showed that the diameter of the fibres ranged between 80-100 nm and contain some beads. The infrared test also showed that the intensity of the peaks decreases after the transformation of polyamide into nanofibric. The resulting surface has the hydrophobic properties, especially after the addition of Titanium nanoparticles.
Min/max on-chip inductance models and delay metrics

This paper proposes an analytical inductance extraction model for characterizing min/max values of typical on-chip global intercon-nect structures, and a corresponding delay metric that can be used to provide RLC delay prediction from physical geometries. The model extraction and analysis is efficient enough to be used within optimization and physical design exploration loops. The analytical min/max inductance approximations also provide insight into the effects caused by inductances.
Camera tracking using concentric circle markers: Paradigms and algorithms

A C2Tag refers to a set of concentric circles of different radii. C2Tags have been recently introduced in computer vision, in particular for camera calibration, as they offer highly interesting photometric and geometric properties, compared to the classical “checkerboard” tags. In this work, we propose the general paradigm of camera tracking based on a planar marker consisting of at least two C2Tags. All the involved steps are described: detection, identification, 2D reconstruction, calibration and 3D reconstruction. Our contribution is to introduce the following missing steps required to deal with long video sequences under time constraints: key-frame selection, bundle adjustment and intermediate pose refinement.
Plantar Plate Repair for Lesser Metatarsophalangeal Joint Instability

Background: Lesser metatarsophalangeal (MTP) joint instability is a common cause of forefoot pain. Advances in operative technique and instrumentation have made it possible to anatomically treat plantar plate tears through a dorsal approach. Our goal was to evaluate the subjective, functional, and radiographic outcomes of plantar plate repair (PPR) from a dorsal approach. Methods: A prospective case series was performed evaluating the results of PPR in 97 feet with 138 plantar plate tears. Patients underwent PPR from a dorsal approach with a Weil osteotomy. We followed patients at regular intervals for 12 months and collected data preoperatively and postoperatively with respect to visual analog scale (VAS) scores, MTP range of motion (ROM), paper pull-out test, American Orthopaedic Foot & Ankle Society (AOFAS) scores, satisfaction, and radiographic measures. Results: Eighty percent of patients scored “good” to “excellent” satisfaction scores at 12 months. The mean VAS pain score preoperatively was 5.4/10, and postoperatively was 1.5/10. The mean AOFAS scores increased from 49 to 81 points following surgery. The mean MTP ROM preoperatively was 43 degrees and postoperatively 31 degrees. Forty-two percent of toes passed the paper pull out test prior to surgery and 54% at 12 months. Mean metatarsal shortening was 2.4/3.1/1.2 mm for the second, third, and fourth metatarsals, respectively. The mean MTP joint angles preoperatively were 2/4.9/–1.3 degrees and postoperatively were 7.4/9.6/0.2 degrees, respectively, for the second, third, and fourth MTP joints. Conclusion: We found that the plantar plate could be repaired through a dorsal approach with reliable outcomes. PPR was a viable option to anatomically restore the ligamentous support in the unstable lesser MTP joint. Level of Evidence: Level IV, retrospective case series.
Mutation of FA2H underlies a complicated form of hereditary spastic paraplegia (SPG35)

Hereditary spastic paraplegia (HSP) describes a heterogeneous group of inherited neurodegenerative disorders in which the cardinal pathological feature is upper motor neurone degeneration leading to progressive spasticity and weakness of the lower limbs. Using samples from a large Omani family we recently mapped a gene for a novel autosomal recessive form of HSP (SPG35) in which the spastic paraplegia was associated with intellectual disability and seizures. Magnetic resonance imaging of the brain of SPG35 patients showed white matter abnormalities suggestive of a leukodystrophy. Here we report homozygous mutations in the fatty acid 2‐hydroxylase gene (FA2H) in the original family used to define the SPG35 locus (p.Arg235Cys) as well as in a previously unreported Pakistani family with a similar phenotype (p.Arg53_Ile58del). Measurement of enzyme activity in vitro revealed significantly reduced enzymatic function of FA2H associated with these mutations. These results demonstrate that mutations in FA2H are associated with SPG35, and that abnormal hydroxylation of myelin galactocerebroside lipid components can lead to a severe progressive phenotype, with a clinical presentation of complicated HSP and radiological features of leukodystrophy. © 2010 Wiley‐Liss, Inc.
Lossless polar compression of q-ary sources

In this paper, lossless polar compression of q-ary memoryless sources in the noiseless setting is investigated. Polar compression scheme for binary memoryless sources, introduced by Cronie and Korada, is generalized to sources over prime-size alphabets. In order to reduce the average codeword length, a compression scheme based on successive cancellation list decoding is proposed. Also, a specific configuration for the compression of correlated sources is considered, and it is shown that the introduced polar compression schemes achieve the corner point of the admissible rate region. Based on this result, proposed compression schemes are extended to arbitrary finite source alphabets by using a layered approach.
Towards a database for genotype-phenotype association research: mining data from encyclopaedia

To associate phenotypic characteristics of an organism to molecules encoded by its genome, there is a need for well-structured genotype and phenotype data. We use a novel method for extracting data on phenotype and genotype characteristics of microorganisms from text. As a resource, we use an encyclopedia of microorganisms, which holds phenotypic and genotypic data and create a structured, flexible data resource, which can be exported to a range of database formats, containing genotype and phenotype data for 2412 species and 873 genera of microbes. This data source has great potential as a resource for future biological research on genotype-phenotype associations. In this paper, we focus on describing the structure and content of the resulting database and on evaluating the method used for extracting the data. We conclude that the resulting database can be used as a reliable complementary resource for research into genotype-phenotype association.
Crack propagation monitoring on bonded joints with novel carbon nanotube doped adhesive films

The use of composite structures has been extended during the last decades due to their good specific properties, especially on aircraft industry. However, the design and monitoring of composites is often complex, especially when joints are considered. In particular, component assembly could be carried out by bolted joints or adhesively. Bonded joints present many advantages in comparison to fastened joints such as a more uniform stress distribution along the bonding line or a weight saving. However, their inspection is not easy and usually requires an expensive maintenance. To date, carbon nanotubes (CNTs) have widely demonstrated their capability for Structural Health Monitoring (SHM) purposes [1,2] due to their piezoresistive behaviour which, combined with their good electrical properties, makes their use as strain sensors possible by measuring the electrical resistance of the hosting material. In a previous study [3], a novel CNT doped adhesive film has been proposed for monitoring bonded joints at quasi-static load state. Mode-I and single lap shear (SLS) tests have been carried out proving the sensing capabilities of this type of adhesive. In this regard, this work aims to use the proposed CNT/adhesive film to monitoring crack propagation on SLS CFRP specimens. For that purpose, fatigue tests have been carried out while electrical response of adhesive joints has been monitored. In addition, crack length has been measured during the test using a microscope camera. It has been noticed that there is a direct correlation between electrical response and crack length. An increase on voltage across the specimen and, thus, electrical resistance is observed, being this more prevalent in the last cycles of fatigue tests when crack propagation takes places suddenly. Moreover, it is possible to distinguish between uniform crack propagation and stick-slip behaviour based on the electrical response. Therefore, CNT doped adhesive film capability to detect crack initiation and propagation has been demonstrated, proving their huge potential for SHM purposes.