Miracle-dz/UniFAR-FTUs huggingface dataset:
The Identification of Proteoglycans and Glycosaminoglycans in Archaeological Human Bones and Teeth

Bone tissue is mineralized dense connective tissue consisting mainly of a mineral component (hydroxyapatite) and an organic matrix comprised of collagens, non-collagenous proteins and proteoglycans (PGs). Extracellular matrix proteins and PGs bind tightly to hydroxyapatite which would protect these molecules from the destructive effects of temperature and chemical agents after death. DNA and proteins have been successfully extracted from archaeological skeletons from which valuable information has been obtained; however, to date neither PGs nor glycosaminoglycan (GAG) chains have been studied in archaeological skeletons. PGs and GAGs play a major role in bone morphogenesis, homeostasis and degenerative bone disease. The ability to isolate and characterize PG and GAG content from archaeological skeletons would unveil valuable paleontological information. We therefore optimized methods for the extraction of both PGs and GAGs from archaeological human skeletons. PGs and GAGs were successfully extracted from both archaeological human bones and teeth, and characterized by their electrophoretic mobility in agarose gel, degradation by specific enzymes and HPLC. The GAG populations isolated were chondroitin sulfate (CS) and hyaluronic acid (HA). In addition, a CSPG was detected. The localization of CS, HA, three small leucine rich PGs (biglycan, decorin and fibromodulin) and glypican was analyzed in archaeological human bone slices. Staining patterns were different for juvenile and adult bones, whilst adolescent bones had a similar staining pattern to adult bones. The finding that significant quantities of PGs and GAGs persist in archaeological bones and teeth opens novel venues for the field of Paleontology.
CompPhy2: a flexible and real time collaborative web platform for editing and comparing phylogenies

CompPhy2 is a real time collaborative web platform for visualization, comparison and annotation of phylogenetic trees with a responsive user friendly interface. It is the only phylogenetic web platform allowing several users to work synchronously or asynchronously on a same dataset. CompPhy2 brings new features such as side by side comparison, tree annotation, custom display, supertree inference,
Fine retinotopic organization of optic terminal arbors in the tectum of normal goldfish

Although the retinotectal projection of goldfish has long been known to have a high degree of retinotopic order, the structural basis for this in terms of the precise positioning of axonal arbors from neighboring retinal ganglion cells has not been determined. In studying this, a small number of neighboring retinal ganglion cells was selectively labeled by a microinjection of DiI into the retina. Following axoplasmic transport for several days, the tectum was removed and flat-mounted for fluorescence microscopy. The injection labeled a small number of axons and their terminal arbors which ranged in size from 108 × 134 μm to 394 × 331 μm with a mean of 233 × 219 μm. This mean size corresponds to about 1/15 of the length of one tectal axis. Although individual arbors labeled from one small retinal injection were always observed near the same retinotopic position, they were almost never coextensive. Overlap between pairs of arbors along the lines of projection perpendicular to the tectal surface averaged 57% of the area of a single arbor. These results indicate that neighboring retinal ganglion cells do not converge onto the same locus but instead project as a continuous retinotopic array of partially overlapping terminal fields.
A Crispr Knockout Screen Identifies Foxf1 as a Suppressor of Colorectal Cancer Metastasis that Acts through Reduced mTOR Signalling

Introduction A greater understanding of molecular mechanisms underlying metastasis is necessary for development of new strategies to prevent and treat cancer. Methods We performed a genome-wide CRISPR/Cas9 knockout screen in MC38 colorectal cancer (CRC) cells transplanted orthotopically into mice to identify genes that promote metastasis. We undertook focussed molecular analyses to identify mechanisms underlying metastasis. Results The screen identified several gene knockouts over-represented in lung metastases, including Dptor (mTOR signalling) and Foxf1 (gastrointestinal tumour predisposition). We validate that loss of Foxf1 promotes metastasis, increased Foxf1 expression restrained cellular migration in-vitro and human CRC metastases express lower Foxf1 than paired primary tumours. Analysis of gene expression changes downstream of Foxf1 identified increased mTOR signalling as a possible mechanism of metastasis caused by Foxf1 loss, consistent with Dptor identification. We confirmed this mechanism demonstrating that mTOR inhibitor sirolimus reduced lung metastasis burden in xenografts. Conclusion Mesenchymal Foxf1 plays a major role in intestinal development. We have shown for the first time, through an unbiased genetic screen, that reduced epithelial Foxf1 results in raised mTOR signalling and metastasis. Authorship statement Lennard Lee-study concept and design, acquisition of data, analysis, interpretation of data, drafting of the manuscript, statistical analysis and obtained funding. Connor Woolley-acquisition of data, analysis and interpretation of data. Thomas Starkey-acquisition of data, analysis, interpretation of data, drafting of the manuscript. Luke Freeman-Mills-interpretation of data. Andrew Bassett-technical and material support. Fanny Fanchini-technical support. Lai Mun Wang-acquisition of data and study supervision. Annabelle Lewis-study supervision. Roland Arnold-analysis, interpretation of data, statistical analysis. Ian Tomlinson-study supervision and critical revision of the manuscript. Conflict of Interest The authors whose names are listed above declare that they have no conflict of interest.
Bortezomib Plus Gemcitabine/Carboplatin as First-Line Treatment of Advanced Non-small Cell Lung Cancer: A Phase II Southwest Oncology Group Study (S0339)

Introduction: Bortezomib is a small-molecule proteasome inhibitor with single-agent activity in patients with non-small cell lung carcinoma (NSCLC) and synergy with gemcitabine in preclinical studies. This phase II study of bortezomib in combination with gemcitabine/carboplatin was conducted in chemotherapy-naive advanced NSCLC patients to assess efficacy and safety. Methods: Patients with selected stage IIIB/IV NSCLC, performance status 0–1, and no history of brain metastasis received up to six 21-day cycles of gemcitabine 1000 mg/m2, days 1 and 8, carboplatin area under curve 5.0, day 1, and bortezomib 1.0 mg/m2, days 1, 4, 8, and 11. Results: One-hundred-fourteen patients (52% adenocarcinoma, 85% stage IV) received a median of 3.6 treatment cycles. Median follow-up was >3 years. Median overall survival was 11 months; 1-year and 2-year survival rates were 47% and 19%, respectively. Median progression-free survival was 5 months; 1-year progression-free survival rate was 7%. Response rate was 23%, and disease control rate (responses + stable disease) was 68%. The most common grade 3/4 toxicities were thrombocytopenia (63%) and neutropenia (52%). One patient experienced febrile neutropenia. Grade 3/4 neuropathy occurred in 4%, and a further 6% experienced grade 2 sensory neuropathy. Conclusions: Bortezomib plus gemcitabine/carboplatin resulted in a notable survival benefit in patients with advanced NSCLC, with the anticipated primary toxicity of myelosuppression. Further studies designed to investigate the role of bortezomib in advanced NSCLC are warranted.
Millimeter Wave LOS Coverage Enhancements with Coordinated High-Rise Access Points

Millimetre wave (mm-wave) communication is considered as one of the most important enablers for the fifth generation communication (5G) system to support data rate of Gbps and above. In some scenarios, it is crucial to maintain a line of sight (LOS) link for users enjoying 5G immersive experiences and thus requiring very high data rate. In this paper, we investigate the LOS probability in mm-wave systems. In particular, we study the impact of access point (AP) and blockage height on the LOS probability and propose a solution to effectively enhance the LOS coverage by using high-rise APs on top of low-rise APs normally installed on street furniture, e.g., lamp poles. Two deployment options are explored: 1) irregular deployment and 2) regular deployment, where LOS probability is derived for both cases. Simulation results show that the impact of AP height on LOS probability is significant and using coordinated high-rise APs jointly deployed with low-rise APs will substantially improve the LOS probability.
Mapping Users across Networks by Manifold Alignment on Hypergraph

Nowadays many people are members of multiple online social networks simultaneously, such as Facebook, Twitter and some other instant messaging circles. But these networks are usually isolated from each other. Mapping common users across these social networks will benefit many applications. Methods based on username comparison perform well on parts of users, however they can not work in the following situations: (a) users choose different usernames in different networks; (b) a unique username corresponds to different individuals. In this paper, we propose to utilize social structures to improve the mapping performance. Specifically, a novel subspace learning algorithm, Manifold Alignment on Hypergraph (MAH), is proposed. Different from traditional semi-supervised manifold alignment methods, we use hypergraph to model high-order relations here. For a target user in one network, the proposed algorithm ranks all users in the other network by their possibilities of being the corresponding user. Moreover, methods based on username comparison can be incorporated into our algorithm easily to further boost the mapping accuracy. Experimental results have demonstrated the effectiveness of our proposed algorithm in mapping users across networks.
Viral Etiologies of Acute Dehydrating Gastroenteritis in Pakistani Children: Confounding Role of Parechoviruses

Despite substantial interventions in the understanding and case management of acute gastroenteritis, diarrheal diseases are still responsible for a notable amount of childhood deaths. Although the rotavirus is known to cause a considerable burden of pediatric diarrheal cases, the roles of other viruses remain undefined for the Pakistani population. This study was based on tertiary care hospital surveillance, from January 2009 to December 2010, including the detection of rotavirus, norovirus, astrovirus, and human parechovirus in children under the age of five using serological or molecular assays. Rotavirus, human parechovirus, norovirus, and astrovirus were detected in 66%, 21%, 19.5%, and 8.5% subjects, respectively. Human parechovirus genotypes, determined through analysis of VP1 gene sequences, showed a great diversity among co-circulating strains. Eighty percent of hospitalized children had dual or multiple viral infections, while 98% parechovirus positive cases were co-infected with rotavirus. The remarkable diversity of viruses associated with the childhood diarrhea in Pakistan calls for large-scale epidemiological surveys, coupled with case control studies, to ascertain their role in clinical manifestations. In addition, these findings also highlight the need for the implementation of up-to-date health interventions, such as the inclusion of a rotavirus vaccine in routine immunization programs for the improvement of quality in child health care.
Serum deprivation‐response protein regulates aldehyde dehydrogenase 1 through integrin‐linked kinase signaling in endometrioid carcinoma cells

Endometrioid carcinoma (EC) is one of the most common malignancies of the female genital system. We reported previously that aldehyde dehydrogenase 1 (ALDH1), a predominant isoform of the ALDH family in mammals and a potential marker of normal and malignant stem cells, is related to the tumorigenic potential of EC. We compared the levels of various proteins in human EC cells with high and low ALDH1 expression using shotgun proteomics and found that serum deprivation‐response protein (SDPR) was preferentially expressed in cells with high ALDH1 expression. Also known as cavin‐2, SDPR is a member of the cavin protein family, which is required for the formation of caveolae. Using SDPR‐knockout EC cells generated using the CRISPR/Cas9 system, we revealed that SDPR was correlated with invasion, migration, epithelial‐mesenchymal transition, and colony formation, as well as the expression of ALDH1. RNA sequencing showed that integrin‐linked kinase (ILK) signaling is involved in the effect of SDPR on ALDH1. Immunohistochemical analysis revealed that the localization of ILK at the cell cortex was disrupted by SDPR knockout, potentially interfering with ILK signaling. Moreover, immunohistochemical analysis of clinical samples showed that SDPR is related to histological characteristics associated with invasiveness, such as poor differentiation, lymphatic invasion, and the microcystic, elongated, and fragmented histopathological pattern. This is, to our knowledge, the first report that SDPR is related to tumor progression.
Towards concept-aware programming environments for guiding software modularity

To design and implement a program, programmers choose analogies and metaphors to explain and understand programmatic concepts. In source code, they manifest themselves as a particular choice of names. During program comprehension, reading such names is an important starting point to understand the meaning of modules and guide the exploration process. On the one hand, understanding a program in depth by looking for names that suggest a particular analogy can be a time-consuming process. On the other hand, a lack of awareness which concepts are present and which analogies have been chosen can lead to modularity issues, such as redundancy and architectural drift if concepts are misaligned with respect to the current module decomposition. In this work-in-progress paper, we propose to integrate first-class concepts into the programming environment. We assign meaning to names by labeling them with a color corresponding to the metaphor or analogy this name was derived from. We hypothesize that aggregating labels upwards along the module hierarchy helps to understand how concepts are distributed across the program, collecting names belonging to a specific concept helps programmers to recognize which metaphor has been chosen, and presenting relations between concepts can summarize complex interactions between program parts. We argue that continuous feedback and awareness of how names are grouped into concepts and where they are located can help preventing modularity issues and ease program comprehension. As a first step towards an implementation, we define criteria that help to detect names belonging to the same concept. We then investigate how techniques from natural language processing can be re-used and modified to compute an initial concept allocation with respect to these criteria. Eventually, we show design sketches how we plan to arrange and present concepts to programmers through tools, and what kind of information they can provide to help programmers make informed implementation decisions.
Glycolysis in Plasmodium falciparum results in modulation of host enzyme activities.

BACKGROUND & OBJECTIVES Plasmodium falciparum, the causative agent of the most serious form of malaria, infects about 5-10% of the world human population per year. It is well established that the erythrocytic stages of the malaria parasite rely mainly on glycolysis for their energy supply. In the present study, the glucose utilisation of erythrocyte population with parasitaemia levels similar to that of malaria patients was measured. The results allowed us to assess the effect of the parasites on the glucose utilisation of the vast majority of uninfected erythrocytes. METHODS Using [2-13C]glucose and nuclear magnetic resonance (NMR) technique, the glucose utilisation in normal red blood cell (RBC) and P. falciparum infected red blood cell (IRBC) populations was measured. The IRBC population consisted of > 96% RBC and < 4% of parasite infected red blood cells (PRBC). The glycolytic enzymes were assayed to assess the effect of infected red cells on the enzymatic activities of uninfected ones. RESULTS The rate of glucose utilisation by IRBC was considerably higher than that of RBC. Upon addition of 25% v/v conditioned culture medium (CM) of IRBC, RBCs exhibited a significant decrease in glucose utilisation. The CM could directly inhibit the activities of RBC glycolytic enzymes-phosphofructokinase (PFK) and pyruvate kinase (PK), without interfering with the activity of the pentose phosphate pathway enzyme-glucose-6-phosphate dehydrogenase (G-6-PD). INTERPRETATION & CONCLUSION The present study showed that the clinical level of P. falciparum infected RBCs (< 4% parasitaemia) significantly enhance the glycolytic flux as well as down-regulate the glucose utilisation rate in the majority of uninfected RBC population. The mechanism of inhibition seems to be direct inhibition of the regulatory glycolytic enzymes-PFK and PK.
Modeling efficiency and robustness in ruminants: the nutritional point of view.

The efficiency and robustness of farm animals has been of growing interest in recent decades, particularly for ruminants which are subject to many constraints. In recent times, systemic modeling approaches have been developed with promising applications in all areas of livestock production.Therefore, the main challenge is to apply modeling methods to issues of efficiency and robustness. Thus, in the domain of animal nutrition, the recent systems of feeding units have proposed interesting advances that will soon be applicable in the field.
Should the democrats move to the left on economic policy

Could John Kerry have gained votes in the 2004 Presidential election by more clearly distinguishing himself from George Bush on economic policy? At first thought, the logic of political preferences would suggest not: the Republicans are to the right of most Americans on economic policy, and so in a one-dimensional space with party positions measured with no error, the optimal strategy for the Democrats would be to stand infinitesimally to the left of the Republicans. The median voter theorem suggests that each party should keep its policy positions just barely distinguishable from the opposition. In a multidimensional setting, however, or when voters vary in their perceptions of the parties' positions, a party can benefit from putting some daylight between itself and the other party on an issue where it has a public-opinion advantage (such as economic policy for the Democrats). We set up a plausible theoretical model in which the Democrats could achieve a net gain in votes by moving to the left on economic policy, given the parties' positions on a range of issue dimensions. We then evaluate this model based on survey data on voters' perceptions of their own positions and those of the candidates in 2004. Under our model, it turns out to be optimal for the Democrats to move slightly to the right but staying clearly to the left of the Republicans' current position on economic issues.
Web-Enhanced Tobacco Tactics With Telephone Support Versus 1-800-QUIT-NOW Telephone Line Intervention for Operating Engineers: Randomized Controlled Trial

Background Novel interventions tailored to blue collar workers are needed to reduce the disparities in smoking rates among occupational groups. Objective The main objective of this study was to evaluate the efficacy and usage of the Web-enhanced “Tobacco Tactics” intervention targeting operating engineers (heavy equipment operators) compared to the “1-800-QUIT-NOW” telephone line. Methods Operating engineers (N=145) attending one of 25 safety training sessions from 2010 through 2012 were randomized to either the Tobacco Tactics website with nurse counseling by phone and access to nicotine replacement therapy (NRT) or to the 1-800-QUIT-NOW telephone line, which provided an equal number of phone calls and NRT. The primary outcome was self-reported 7-day abstinence at 30-day and 6-month follow-up. The outcomes were compared using chi-square tests, t tests, generalized mixed models, and logistic regression models. Results The average age was 42 years and most were male (115/145, 79.3%) and white (125/145, 86.2%). Using an intent-to-treat analysis, the Tobacco Tactics website group showed significantly higher quit rates (18/67, 27%) than the 1-800-QUIT NOW group (6/78, 8%) at 30-day follow-up (P=.003), but this difference was no longer significant at 6-month follow-up. There were significantly more positive changes in harm reduction measures (quit attempts, number of cigarettes smoked per day, and nicotine dependence) at both 30-day and 6-month follow-up in the Tobacco Tactics group compared to the 1-800-QUIT-NOW group. Compared to participants in the 1-800-QUIT NOW group, significantly more of those in the Tobacco Tactics website group participated in the interventions, received phone calls and NRT, and found the intervention helpful. Conclusions The Web-enhanced Tobacco Tactics website with telephone support showed higher efficacy and reach than the 1-800-QUIT-NOW intervention. Longer counseling sessions may be needed to improve 6-month cessation rates. Trial Registration Clinicaltrials.gov NCT01124110; http://clinicaltrials.gov/ct2/show/NCT01124110 (Archived by WebCite at http://www.webcitation.org/6TfKN5iNL).
Thirty-Second Walk Test: Expansion of Normative Data

Purpose: To collect 30-second walk test (30sWT) normative data on a large, diverse sample of school children developing typically, ages 5 to 13 years, and describe the influences of gender, body mass index, and path shape on distance walked. Methods: Five physical therapists administered the 30sWT on 1223 children developing typically (boys = 517, girls = 706) from 20 urban schools. Results: Average distances (standard deviation) ranged from 139.1 (20.3) to 163.0 (18.6) ft; children aged 10 years walked the farthest and those aged 5 years the shortest. Distance steadily increased from ages 5 to 10 years, steadily decreased from ages 11 to 13 years; children aged 8, 9, and 10 years had statistical but not functionally meaningful gender differences. Body mass index and path shape had no meaningful effects. Distance and velocities are similar to prior studies. Conclusion: This study updated 30sWT normative values with a large, ethnically diverse, urban sample developing typically. Norms may be useful as part of a comprehensive examination.
Appearance Enhancement for Visually Impaired with Projector Camera Feedback

—Visually impaired is a common problem for human life in the world wide. The projector-based AR technique has ability to change appearance of real object, and it can help to improve visibility for visually impaired. We propose a new framework for the appearance enhancement with the projector camera system that employed model predictive controller. This framework enables arbitrary image processing such as photo-retouch software in the real world and it helps to improve visibility for visually impaired. In this article, we show the appearance enhancement result of Peli’s method and Wolffshon’s method for the low vision, Jefferson’s method for color vision deﬁciencies. Through experiment results, the potential of our method to enhance the appearance for visually impaired was conﬁrmed as same as appearance enhancement for the digital image and television viewing.