Miracle-dz/UniFAR-FTUs huggingface dataset:
Surgical approaches for the treatment of perihilar cholangiocarcinoma

ABSTRACT Introduction: Since their initial description, perihilar cholangiocarcinoma (pCCA) has remained one of the more clinically challenging scenarios encountered by hepatobiliary surgeons. Surgery remains the only potentially curative therapy, but requires complex, technically demanding operations with high associated morbidity and mortality. Over the last several decades, advances in surgical technique and perioperative management have improved patient outcomes. Areas covered: Achievement of optimal outcomes requires a multidisciplinary approach from a team of providers with expertise in hepatobiliary and oncologic surgery, medical oncology, radiation oncology, and advanced gastroenterology. We herein report a comprehensive review on pCCA with an emphasis on surgical strategies and perioperative management. Expert commentary: Despite incremental improvements from advances in surgical technique and perioperative management, outcomes remain poor due to the aggressive systemic nature of this disease and the tendency for locoregional and distant recurrence. The marginal benefit observed with traditional systemic therapies continues to be a key weakness in current management. However, improved understanding of the genetic alterations and pathways that drive tumorigenesis has the potential to dramatically alter the way in which we care for these patients.
Case presentation and short perspective on management of foraminal/far lateral discs and stenosis

Background: The management of lumbar foraminal/far lateral discs (FOR/FLD) with stenosis remains controversial. Operative choices should be based on each patient's preoperative dynamic X-ray findings, magnetic resonance (MR), and computed tomography (CT) studies. Here we reviewed several options for decompression alone vs. decompression with fusion. Methods: Safe excision of FOR/FLD with stenosis should begin at the level above the disc herniation, as identification of the superior, foraminally, and far laterally exiting nerve root is critical. Performing an undercutting laminectomy and utilizing an operating microscope usually preserves the facet joints, and in many cases, avoids the need for fusion. Other decompressive techniques include; the intertransverse (ITT), and Wiltse approaches. Fusions following complete unilateral full facetectomy may be; noninstrumented (e.g., older, osteoporotic patients) vs. instrumented (e.g., posterolateral fusion or occasionally transforaminal lumbar interbody fusion). Here we present a patient with L2-L5 stenosis, and a left L3-L4 FOR/FLD, and multiple synovial cysts who was successfully managed with an l2-L5 laminecotmy, left L34 FOR/FLD diksectomy without fusion. Results: Postoperatively, the patient was neurologically intact, and stability was maintained. Adjunctive measures for FOR/FLD diksectomy should include; intraoperative monitoring, use of the operating microscope, and an intraoperative film with a radiopaque marker in the correct disc space to confirm the correct level of diskectomy. Conclusions: There are multiple approaches to the excision of FOR/FLD with stenosis. These include; decompression alone vs. decompression with non-instrumented vs. instrumented fusion. Surgical choices must be based on individual patient's X-ray, MR, and CT findings. The aim should be to maximize the safety of disc excision with decompression of stenosis, and to preserve stability, reducing the need for fusion, while minimizing morbidity.
Multiple testing with discrete data: Proportion of true null hypotheses and two adaptive FDR procedures

We consider multiple testing with false discovery rate (FDR) control when p values have discrete and heterogeneous null distributions. We propose a new estimator of the proportion of true null hypotheses and demonstrate that it is less upwardly biased than Storey's estimator and two other estimators. The new estimator induces two adaptive procedures, that is, an adaptive Benjamini–Hochberg (BH) procedure and an adaptive Benjamini–Hochberg–Heyse (BHH) procedure. We prove that the adaptive BH (aBH) procedure is conservative nonasymptotically. Through simulation studies, we show that these procedures are usually more powerful than their nonadaptive counterparts and that the adaptive BHH procedure is usually more powerful than the aBH procedure and a procedure based on randomized p‐value. The adaptive procedures are applied to a study of HIV vaccine efficacy, where they identify more differentially polymorphic positions than the BH procedure at the same FDR level.
An Algorithm to Compute Protein Homology Based On Hydrophobic Cluster Analysis

Current techniques in protein homology testing involve a 1-dimensional alignment of Nucleotide or Amino acid sequencing. Due to its various constraints and low sequence identity values, a 2-Dimensional Hydrophobic Cluste r Alignment has increasingly been used to predict the structure and functionality of protein. This work proposed an algorithm based on a secondary-structure Hydrophobic Cluster Alignment to compute a similarity score of protein sequences aut omatically, which helps reduce interventions of a human expert for a manual alignment. Additional techniques are introduced to speed up the calculation, as well as to resolve some greedy-base d alignment limitation in the previous work. The alignment results and the classification accuracies from the well-known HOMSTRAD database have demonstrated an improvement in both a ccuracy and the computation time. Keywords-bioinformatic; hydrophobic cluster analysis; protien homology; automatic alignment
Comparative Study of Two Systems for the Assessment of Static Balance in Veterans with Mild Traumatic Brain Injury

Background Traditionally, the diagnosis of postural instability relies on the clinical examination of static balance. In recent years, computerized technologies have provided a new approach for the accurate detection of positional changes during functional balance. Aim The aim of this study was to investigate the similarities and differences between two electronic systems, NeuroCom and BioSensics, and their application in the clinical assessment of impaired balance in American veterans. Materials and Methods We examined the sway around the center of mass during static balance conditions in 25 veterans with mild traumatic brain injury, using the two electronic systems. These patients met the inclusion criteria and were assessed for their impaired balance at the District of Columbia Veterans Affair Medical Center, Washington, DC, USA. Results There were six static balance tests conducted on either NeuroCom or BioSensics system in triplicate. Of the data for 36 sets of statistical data analyses, there were significant correlations among those for eight data sets (22.2%) between the two systems. The strongest positive correlation between the data from the two systems was found during the baseline test, when inputs from visual, vestibular and sensorymotor sources were uninterrupted. The data from the remaining experimental conditions did not correlate significantly with one another. Conclusions Both NeuroCom and BioSensics provided comparable data in eight out of 36 experimental conditions in the assessment of static balance in patients with mild traumatic brain injury. The findings clarified the ambiguities in the application of NeuroCom versus BioSensics, provided new knowledge for the field of physical medicine and rehabilitation, and improved the clinical assessment of static balance in patients with mTBI.
Honey Antibacterial Effect Boosting Using Origanum vulgare L. Essential Oil

The appearance of new bacterial strains which cause pathogenic diseases and which are resistant to the most used antibiotics requires probing new antibacterial agents sources. Therefore, the main aim of the present work was to follow the antibacterial activity of honey samples from Palestine and Morocco, after the combination with Origanum vulgare L. essential oil, and figure out whether the honey physicochemical parameters and geographic origin influence the final activity. The results of this study showed good geographical discrimination between the Palestinians and Moroccan honey samples. The antioxidant and antimicrobial activities showed a significant correlation with honey color, melanoidins, and phenolic and flavonoids contents. Furthermore, the possible effect of honey physicochemical parameters on the gained antimicrobial activities was assessed using the principal component analysis (PCA). Some parameters showed a promising effect and seem to be important in the process of honey samples selection. Namely, melanoidins content, phenolic content, electrical conductivity, and mineral content were shown to be positively influencing the gained antibacterial activity after the combination with essential oil against the tested strains, although a significant negative correlation was seen with the FIC only in the case of Escherichia coli (ATB: 57).
Effects of Ethanol on Sensory Inputs to the Medial Giant Interneurons of Crayfish

Crayfish are capable of two rapid, escape reflexes that are mediated by two pairs of giant interneurons, the lateral giants (LG) and the medial giants (MG), which respond to threats presented to the abdomen or head and thorax, respectively. The LG has been the focus of study for many decades and the role of GABAergic inhibition on the escape circuit is well-described. More recently, we demonstrated that the LG circuit is sensitive to the acute effects of ethanol and this sensitivity is likely mediated by interactions between ethanol and the GABAergic system. The MG neurons, however, which receive multi-modal sensory inputs and are located in the brain, have been less studied despite their established importance during many naturally occurring behaviors. Using a combination of electrophysiological and neuropharmacological techniques, we report here that the MG neurons are sensitive to ethanol and experience an increase in amplitudes of post-synaptic potentials following ethanol exposure. Moreover, they are affected by GABAergic mechanisms: the facilitatory effect of acute EtOH can be suppressed by pretreatment with a GABA receptor agonist whereas the inhibitory effects resulting from a GABA agonist can be occluded by ethanol exposure. Together, our findings suggest intriguing neurocellular interactions between alcohol and the crayfish GABAergic system. These results enable further exploration of potentially conserved neurochemical mechanisms underlying the interactions between alcohol and neural circuitry that controls complex behaviors.
Designing Gamified E-Learning Applications for Children with Down's Syndrome - The Case of Teaching Literacy and Language Skills

Down’s syndrome (DS) is the most common genetic cause of intellectual disability worldwide, with language being one of the most affected area. Language skills and literacy acquisition thus require special care. It is still rare to use software to support such care while, simultaneously, providing education and entertainment. This paper presents results of research on the design of gamified software applications to support pedagogical processes of literacy and language acquisition, making them fun, motivating and effective for children with DS. The paper analyses rankings of design domains of gamified e-learning applications done earlier in the research according to pedagogical benefits in entertaining education of DS children. The paper is believed to offer contributions to requirements engineering of e-learning, gamified software applications in general and to computer-assisted education of DS children in particular. The paper directly contributes to the concretization of article 24 (access to Education) of the General Principles, Accessibility, of the United Nations Convention on the Rights of Persons with Disabilities (UNCRPD). Usage of applications that implement most beneficial requirements may also indirectly contribute to UNCRPD article 19 –Living independently and being included in the community; article 21 – access to Information and communication services; and, article 27 Work and employment.
Retrospective study on the hygienic quality of fresh ricotta cheeses produced in Sicily, Italy

The present work was carried out to investigate the microbiological profile of Sicilian ewes’ ricotta cheeses during fifteen years of investigations (2002-2016). The samples were collected between those conferred to the Istituto Zooprofilattico Sperimentale della Sicilia (IZSSi) Adelmo Mirri, Palermo (Italy), by the competent authority during official control, by food business operator in HACCP systems and in research projects. Enterobacteriaceae, Escherichia coli and coagulase-positive staphylococci (CPS) were found only in some samples. Bacillus cereus was detected in c.a. 16% of samples but the level of contaminations did not reach the threshold that leads to significant toxin production. Pathogenic bacteria such as Listeria monocytogenes, Salmonella spp. and Brucella spp. were never detected. Furthermore, a total of 47 of lactic acid bacteria (LAB) strains were identified at species level by sequencing the 16S rRNA gene, resulting in the identification of 10 species belonging to four genera Enterococcus, Lactobacillus, Lactococcus and Leuconostoc, commonly employed as starter and non starter cultures in different traditional cheese. Results of this study highlighted an improvement of the hygienic conditions of the Sicilian ewes’ ricotta cheeses during the last ten years of investigation. This observation was confirmed from reduction of undesired microorganisms such as Enterobacteriaceae, E.coli and CPS, used to define the process hygiene criteria. However, in order to improve the final quality of this product are needed further strategy such as the dairy makers training, with the aim to apply a good hygienic practices during the production.
A newly discovered column in the hieroglyphic text on La Mojarra Stela 1 : A test of the Epi-Olmec decipherment

A badly weathered column of hieroglyphs was discovered in November 1995 on the side of Stela 1 from La Mojarra in southern Veracruz, Mexico. Most of the signs in this column have now been identified by nighttime examination under artificial lighting, making possible a nearly complete transcription and translation of this column. This data expands the modest corpus of epi-Olmec hieroglyphic texts and confirms various aspects of the decipherment of the epi-Olmec script.
Temporal evolution of the polarization state of optical pulses under the effect of polarization-mode dispersion

The temporal evolution of the polarization state of optical pulses under the effect of polarization-mode dispersion (PMD) is analyzed. Pulse chirp and PMD cause characteristic rotation of the Stokes vector on the Poincare sphere. A dynamical equation describing the rotation is obtained for a Gaussian shaped pulse with linear chirp affected by first-order PMD. Differential group delay, pulsewidth, and first-order frequency chirp are calculated from the measured time-resolved Stokes vector using the dynamical equation.
A Thin Layer Imaging with the Total Internal Reflection Fluorescence Microscopy

Total internal reflection fluorescence microscopy (TIRFM) is an optical technique that allows imaging of a thin layer of the sample with a thickness of about 100-200 nm. It is used in science of cell biology to study cellular processes, especially near the membranes of living cells. This method is based on the total internal reflection phenomenon, where the evanescent wave is generated in the less dense medium. In fact, the evanescent wave is used to illuminate the sample. Consequently, the possibility of observing a superficial (instead of bulk) part of fluorophore labeled sample is opened up. In this work, a total internal reflection fluorescence microscope based on the light guide has been designed and assembled by means of the inverted microscope to image a thin layer from the surface of the sample. Operated experimental arrangement has been employed for the total internal reflection fluorescence imaging of cadmium selenide (CdSe) quantum dots.
How Do People Judge Meaning in Goal-Directed Behaviors: The Interplay Between Self-Concordance and Performance

Perceived performance and self-concordance are two sources of information people may utilize to judge meaning in goal-directed behaviors. We contend that either variable can adequately support the presence of meaning, even in the absence of the other. This perspective suggests that non-self-concordant goal pursuits can feel meaningful as long as one feels successful at the goals, and that failed goal pursuits can feel meaningful as long as they are self-concordant. Five studies investigated this potential interaction between performance and self-concordance. As hypothesized, we found a negative interactive pattern such that meaning was maintained when either performance or self-concordance was high. This interactive effect held true for the experience of meaning in personal goals (Studies 1 and 2), courses (Study 3), and work (Studies 4 and 5). This interactive pattern did not emerge when the outcome variable was either positive affect or job satisfaction, suggesting this compensation process was somewhat unique to meaning.
The Effect of Different Doses of Extracorporeal Shock Waves on Experimental Model Mandibular Distraction

Objective: Distraction osteogenesis (DO) is widely used treatment for the bone deformities. In addition extracorporeal shock wave therapy (ESWT) is a new perspective on noninvasive modalities of management of the bone regeneration. We examined the effects of 2 different single doses of ESWT on the consolidation period of DO of the rabbit mandible using stereological, radiological and immunohistochemical methods in the present study. Methods: DO was performed unilaterally in the mandible of 18 New Zealand rabbits (6 months’ old, weighing between 2.5 and 3 kg). The distraction zone of the mandible has received no treatment as controls. Group 2 (ESWT 500) received ESWT (single dose of 500 impulses 0.19 mJ/mm2 energy flux intensity and 2155 mJ totally) were applied on the first day of the consolidation. Group 3 (ESWT 1000) treated with ESWT (single dose of 1000 impulses0.19 mJ/mm2 energy flux intensity and 4310 mJ totally) were applied on the first day of the consolidation period. After the sacrification, radiologically bone mineral density, new bone formation, new fibrous tissue, and new vessel formation were analyzed using unbiased stereological methods. Results: It was found a statistically significant difference between the study groups and control group in the bone mineral density measurements and the highest values were in the ESWT1000 group. In terms of stereological analysis, there was a significant difference between the study groups and control group (P = 0.00). The new capillary volume was highest in the E1000 group. Additionally, significant differences were found in point of the capillary volumes between the groups control and ESWT500 (P = 0.001), control and ESWT1000 (P = 0.000), ESWT500 and ESWT1000 (P = 0.040), respectively. Conclusions: A total of 1000 impulses ESWT may induce the growth factors to enhance the newly formed bone regeneration.
Molecular engineering of Rashba spin-charge converter

Researchers report the discovery of a way for molecular engineering of Rashba spin-orbit devices. In heterostructures with broken inversion symmetry, the electrons’ motion is coupled to their spin through interface-driven spin-orbit coupling: the Rashba effect. The Rashba effect enables the interconversion between spin and charge currents, offering a variety of novel spintronic phenomena and functionalities. However, despite the significant progress in Rashba physics, controlling the spin-charge conversion in metallic heterostructures remains a major challenge. We show that molecular self-assembly provides a way to engineer the Rashba spin-charge converters. We demonstrate that magnetoresistance and voltage generation originating from the spin-charge conversion in metallic heterostructures can be manipulated by decorating the surface with self-assembled organic monolayers through the cooperative molecular field effect. We also demonstrate reversible phototuning of the spin-charge conversion through light-driven molecular transformations using a molecule that can photoisomerize between the trans and cis states. These findings, with the almost-infinite chemical tunability of organic monolayers, pave the way toward molecular engineering of spin-orbit devices.
SOX2 Drives Bronchial Dysplasia in a Novel Organotypic Model of Early Human Squamous Lung Cancer

Rationale: Improving the early detection and chemoprevention of lung cancer are key to improving outcomes. The pathobiology of early squamous lung cancer is poorly understood. We have shown that amplification of sex‐determining region Y‐box 2 (SOX2) is an early and consistent event in the pathogenesis of this disease, but its functional oncogenic potential remains uncertain. We tested the impact of deregulated SOX2 expression in a novel organotypic system that recreates the molecular and microenvironmental context in which squamous carcinogenesis occurs. Objectives: (1) To develop an in vitro model of bronchial dysplasia that recapitulates key molecular and phenotypic characteristics of the human disease; (2) to test the hypothesis that SOX2 deregulation is a key early event in the pathogenesis of bronchial dysplasia; and (3) to use the model for studies on pathogenesis and chemoprevention. Methods: We engineered the inducible activation of oncogenes in immortalized bronchial epithelial cells. We used three‐dimensional tissue culture to build an organotypic model of bronchial dysplasia. Measurements and Main Results: We recapitulated human bronchial dysplasia in vitro. SOX2 deregulation drives dysplasia, and loss of tumor promoter 53 is a cooperating genetic event that potentiates the dysplastic phenotype. Deregulated SOX2 alters critical genes implicated in hallmarks of cancer progression. Targeted inhibition of AKT prevents the initiation of the dysplastic phenotype. Conclusions: In the appropriate genetic and microenvironmental context, acute deregulation of SOX2 drives bronchial dysplasia. This confirms its oncogenic potential in human cells and affords novel insights into the impact of SOX2 deregulation. This model can be used to test therapeutic agents aimed at chemoprevention.
LA3: A Scalable Link- and Locality-Aware Linear Algebra-Based Graph Analytics System

This paper presents LA3 , a scalable distributed system for graph analytics. LA3 couples a vertex-based programming model with a highly optimized linear algebra-based engine. It translates any vertex-centric program into an iteratively executed sparse matrix-vector multiplication (SpMV). To reduce communication and enhance scalability, the adjacency matrix representing an input graph is partitioned into locality-aware 2D tiles distributed across multiple processes. Alongside, three major optimizations are incorporated to preclude redundant computations and minimize communication. First, the link-based structure of the input graph is exploited to classify vertices into diﬀerent types. After-wards, vertices of special types are factored out of the main loop of the graph application to avoid superﬂuous computations. We refer to this novel optimization as computation ﬁltering . Second, a communication ﬁltering mechanism is involved to optimize for the high sparsity of the input matrix due to power-law distributions, common in real-world graphs. This optimization ensures that each process receives only the messages that pertain to non-zero entries in its tiles, substantially reducing communication traﬃc since most tiles are highly sparse. Lastly, a pseudo-asynchronous computation and communication optimization is proposed, whereby processes progress and communicate asynchronously, consume messages as soon as they become available, and block otherwise. We implemented and extensively tested LA3 on private and public clouds. Results show that LA3 outperforms six related state-of-the-art and popular distributed graph analytics systems by an average