Miracle-dz/UniFAR-FTUs huggingface dataset:
NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods

There is rising evidence of an inverse association between chronic diseases and diets characterized by rich fruit and vegetable consumption. Dietary components may act directly or indirectly on the human genome and modulate multiple processes involved in disease risk and disease progression. However, there is currently no exhaustive resource on the health benefits associated to specific dietary interventions, or a resource covering the broad molecular content of food. Here we present the first release of NutriChem, available at http://cbs.dtu. dk/services/NutriChem-1.0, a database generated by text mining of 21 million MEDLINE abstracts for information that links plant-based foods with their small molecule components and human disease phenotypes. NutriChem contains text-mined data for 18478 pairs of 1772 plant-based foods and 7898 phytochemicals, and 6242 pairs of 1066 plant-based foods and 751 diseases. In addition, it includes predicted associations for 548 phytochemicals and 252 diseases. To the best of our knowledge this database is the only resource linking the chemical space of plant-based foods with human disease phenotypes and provides a foundation for understanding mechanistically the consequences of eating behaviors on health.
Lessons From Practice: Risk of CIN 3 or Cancer Associated With an LSIL or HPV-Positive ASC-US Screening Result in Women Aged 21 to 24

Objective. To characterize the risks of cervical intraepithelial neoplasia 3 (CIN 3) and cancer in women aged 21 to 24 with human papillomavirus (HPV)-positive atypical squamous cells of undetermined significance (ASC-US) and low-grade squamous intraepithelial lesion (LSIL) screening results in routine clinical practice. Materials and Methods. Quality assurance databases containing records of screening test and histologic findings from the Regional Laboratory of the Northern California Kaiser Permanente Medical Care Program were reviewed. Numbers of LSIL and HPV-positive ASC-US results and associated cancers and CIN 3 in women aged 21 to 24 during 2003 to 2007 were tabulated, and the corresponding risks were calculated overall and by year of age. Results. During the 5-year period from 2003 to 2007, 1,620 HPV-positive ASC-US and 2,175 LSIL were diagnosed in women aged 21 to 24, for which corresponding histologic finding is available. No invasive cancers were detected in association with LSIL and HPV-positive ASC-US screening results in this age group during this period. The risk of cancer was therefore 0% (95% CI = 0.00%-0.10%). The risk of CIN 3 associated with an HPV-positive ASC-US was 2.90% (95% CI = 2.14%-3.84%), with LSIL was 2.44% (95% CI = 1.83%-3.18%), and, for the 2 combined, the risk was 2.64% (95% CI = 2.15%-3.20%). Conclusions. The risk of CIN 3 and cancer is low enough that management of women aged 21 to 24 with ASC-US and LSIL smears without immediate colposcopy should be considered, as is currently recommended for women aged 20 and younger.
Functional characterization of rs2229094 (T>C) polymorphism in the tumor necrosis factor locus and lymphotoxin alpha expression in human retina: the Retina 4 project

Purpose The objective of this study is to determine the expression and localization of lymphotoxin alpha (LTA) in human retinas and the functionality of one of its polymorphisms rs2229094 (C13R) (T>C), previously associated with proliferative vitreoretinopathy (PVR) development. Materials and methods Total RNA from three healthy human retinas were extracted and subjected to reverse transcription-polymerase chain reaction (RT-PCR) analysis, using flanking primers of LTA cDNA. In addition, three human eyes with retinal detachment (RD) and three healthy control eyes were subjected to immunohistochemistry (IHC) with a specific antibody against LTA. The functionality of T and C alleles was assessed by using pCEFL-Flag expression vector and transient transfection assays in COS-1 cell line. In addition, expression analysis by RT-PCR, Western blot and subcellular localization of both alleles and by immunofluorescence assay was performed. Results RT-PCR analysis revealed no significant levels of messenger RNA (mRNA) LTA in healthy human retinas. Sequential IHC staining showed differences between healthy human and RD retinas. No differences in mRNA and protein expression levels and in subcellular localization between both alleles were found. Both alleles were located in the cytoplasm of COS-1 cells. Conclusion Although results suggest lack of functionality, the differences found in IHC study and its strong association with PVR and its relationship with tumor necrosis factor locus, warrant further studies and could justify the use of this polymorphism as a valid biomarker to identify high-risk patients to develop PVR after RD.
Genotyping validates photo‐identification by the head scale pattern in a large population of the European adder (Vipera berus)

Abstract Capture‐mark‐recapture procedures are a basic tool in population studies and require that individual animals are correctly identified throughout their lifetime. A method that has become more and more popular uses photographic records of natural markings, such as pigmentation pattern and scalation configuration. As with any other marking tool, the validity of the photographic identification technique should be evaluated thoroughly. Here, we report on a large‐scale double‐marking study in which European adders (Vipera berus) were identified by both microsatellite genetic markers and by the pattern of head scalation. Samples that were successfully genotyped for all nine loci yielded 624 unique genotypes, which matched on a one‐to‐one basis with the individual assignments based on the head scalation pattern. Thus, adders considered as different individuals by their genotypes were also identified as different individuals by their head scalation pattern, and vice versa. Overall, variation in the numbers, shape, and arrangement of the head scales enabled us to distinguish among 3200+ photographed individual snakes. Adders that were repeatedly sequenced genetically over intervals of 2–3 years showed no indication whatsoever for a change in the head scale pattern. Photographic records of 900+ adders that were recaptured over periods of up to 12 years showed a very detailed and precise match of the head scale characteristics. These natural marks are thus robust over time and do not change during an individual's lifetime. With very low frequency (0.3%), we detected small changes in scalation that were readily discernible and could be attributed to physical injury or infection. Our study provides a conclusive validation for the use of photo‐identification by head scale patterns in the European adder.
A message-passing approach for recurrent-state epidemic models on networks

Epidemic processes are common out-of-equilibrium phenomena of broad interdisciplinary interest. Recently, dynamic message-passing (DMP) has been proposed as an efficient algorithm for simulating epidemic models on networks, and in particular for estimating the probability that a given node will become infectious at a particular time. To date, DMP has been applied exclusively to models with one-way state changes, as opposed to models like SIS and SIRS where nodes can return to previously inhabited states. Because many real-world epidemics can exhibit such recurrent dynamics, we propose a DMP algorithm for complex, recurrent epidemic models on networks. Our approach takes correlations between neighboring nodes into account while preventing causal signals from backtracking to their immediate source, and thus avoids "echo chamber effects" where a pair of adjacent nodes each amplify the probability that the other is infectious. We demonstrate that this approach well approximates results obtained from Monte Carlo simulation and that its accuracy is often superior to the pair approximation (which also takes second-order correlations into account). Moreover, our approach is more computationally efficient than the pair approximation, especially for complex epidemic models: the number of variables in our DMP approach grows as 2mk where m is the number of edges and k is the number of states, as opposed to mk^{2} for the pair approximation. We suspect that the resulting reduction in computational effort, as well as the conceptual simplicity of DMP, will make it a useful tool in epidemic modeling, especially for high-dimensional inference tasks.
Raising high-density lipoprotein cholesterol with reduction of cardiovascular risk: the role of nicotinic acid – a position paper developed by the European Consensus Panel on HDL-C*

SUMMARY Reduction of low-density lipoprotein cholesterol (LDL-C) is presently the primary focus of lipid-lowering therapy for prevention and treatment of coronary heart disease (CHD). However, the high level of residual risk among statin-treated patients in recent coronary prevention studies indicates the need for modification of other major components of the atherogenic lipid profile. There is overwhelming evidence that a low plasma level of high-density lipoprotein cholesterol (HDL-C) is an important independent risk factor for CHD. Moreover, a substantial proportion of patients with or at risk of developing premature CHD typically exhibit distinct lipid abnormalities, including low HDL-C levels. Thus, therapeutic intervention aimed at raising HDL-C, within the context of reducing global cardiovascular risk, would benefit such patients, a viewpoint increasingly adopted by international treatment guidelines.
Preventing surgical-site infections in nasal carriers of Staphylococcus aureus.

BACKGROUND Nasal carriers of Staphylococcus aureus are at increased risk for health care-associated infections with this organism. Decolonization of nasal and extranasal sites on hospital admission may reduce this risk. METHODS In a randomized, double-blind, placebo-controlled, multicenter trial, we assessed whether rapid identification of S. aureus nasal carriers by means of a real-time polymerase-chain-reaction (PCR) assay, followed by treatment with mupirocin nasal ointment and chlorhexidine soap, reduces the risk of hospital-associated S. aureus infection. RESULTS From October 2005 through June 2007, a total of 6771 patients were screened on admission. A total of 1270 nasal swabs from 1251 patients were positive for S. aureus. We enrolled 917 of these patients in the intention-to-treat analysis, of whom 808 (88.1%) underwent a surgical procedure. All the S. aureus strains identified on PCR assay were susceptible to methicillin and mupirocin. The rate of S. aureus infection was 3.4% (17 of 504 patients) in the mupirocin-chlorhexidine group, as compared with 7.7% (32 of 413 patients) in the placebo group (relative risk of infection, 0.42; 95% confidence interval [CI], 0.23 to 0.75). The effect of mupirocin-chlorhexidine treatment was most pronounced for deep surgical-site infections (relative risk, 0.21; 95% CI, 0.07 to 0.62). There was no significant difference in all-cause in-hospital mortality between the two groups. The time to the onset of nosocomial infection was shorter in the placebo group than in the mupirocin-chlorhexidine group (P=0.005). CONCLUSIONS The number of surgical-site S. aureus infections acquired in the hospital can be reduced by rapid screening and decolonizing of nasal carriers of S. aureus on admission. (Current Controlled Trials number, ISRCTN56186788.)
THE RADIAL DISTRIBUTION OF H2 AND CO IN TW HYA AS REVEALED BY RESOLVED ALMA OBSERVATIONS OF CO ISOTOPOLOGUES

CO is widely used as a tracer of molecular gas. However, there is now mounting evidence that gas phase carbon is depleted in the disk around TW Hya. Previous efforts to quantify this depletion have been hampered by uncertainties regarding the radial thermal structure in the disk. Here we present resolved ALMA observations of 13CO 3-2, C18O 3-2, 13CO 6-5, and C18O 6-5 emission in TW Hya, which allow us to derive radial gas temperature and gas surface density profiles, as well as map the CO abundance as a function of radius. These observations provide a measurement of the surface CO snowline at ∼30 AU and show evidence for an outer ring of CO emission centered at 53 AU, a feature previously seen only in less abundant species. Further, the derived CO gas temperature profile constrains the freeze out temperature of CO in the warm molecular layer to < 21 K. Combined with the previous detection of HD 1-0, these data constrain the surface density of the warm H2 gas in the inner ∼30 AU such that Σ warm gas = 4.7 − 2.9 + 3.0 g cm − 2 ( R / 10 au ) − 1 / 2 . We find that CO is depleted by two orders of magnitude from R = 10 – 60 AU , with the small amount of CO returning to the gas phase inside the surface CO snowline insufficient to explain the overall depletion. Finally, this new data is used in conjunction with previous modeling of the TW Hya disk to constrain the midplane CO snowline to 17–23 AU.
with anterior communicating artery aneurysms and a son with a ' saccular ' aneurysm

The occurrence of familial cerebral aneurysms lends support to the importance of congenital factors in their pathogenesis. The information on the subject is, however, still meagre, there being less than 20 reports in literature. Earlier literature mentions the occurrence of cerebrovascular accidents in members of the same family with polycystic kidneys (Dunger, 1904). Tonnis and Lange-Cosack (1953) reported angiomas in several members of one family. O'Brien (1942) reported a case with a middle cerebral artery aneurysm whose twin brother might have died from an 'acute cerebrovascular episode' eight years previously. Sudden death in identical twins from such diseases was described by Jokl and Wolffe (1954), but at necropsy evidence was lacking in their report. In the same year, Chambers, Harper, and Simpson (1954) reported proven ruptured aneurysms in father and son, on the middle cerebral artery and the anterior communicating artery respectively. In Bruce's revision of Wilson's Neurology (Wilson, 1955), similar mention is made of 'evidence of their dysplastic origin is afforded by occasional appearance in more than one member of a family', without further details. Walton (1956)described six instances of familial subarachnoid haemorrhage, but no specific details were given. Ross (1959) described a woman with left parieto-occipital angioma and left middle cerebral artery aneurysm whose mother had died of a recurrent subarachnoid haemorrhage after ligation of the carotid artery for a posterior communicating artery aneurysm. Ullrich and Sugar (1960) reported similar disorders in a man with a middle cerebral artery aneurysm whose brother had died after surgery for an anterior communicating artery aneurysm, two brothers who had middle cerebral artery aneurysms on opposite sides of head, a man with multiple (four) aneurysms whose brother had died of a 'cerebkal haemorrhage' (no necropsy) and the brother's son had also died after subarachnoid haemorrhage due to an aneurysm at the junction of the anterior cerebral and the anterior communicating arteries, and a brother-sister pair with internal carotid artery
Algorithms for provisioning virtual private networks in the hose model

Virtual Private Networks (VPNs) provide customers with predictable and secure network connections over a shared network. The recently proposed hose model for VPNs allows for greater flexibility since it permits traffic to and from a hose endpoint to be arbitrarily distributed to other endpoints. In this paper, we develop novel algorithms for provisioning VPNs in the hose model. We connect VPN endpoints using a tree structure and our algorithms attempt to optimize the total bandwidth reserved on edges of the VPN tree. We show that even for the simple scenario in which network links are assumed to have infinite capacity, the general problem of computing the optimal VPN tree is NP hard. Fortunately, for the special case when the ingress and egress bandwidths for each VPN endpoint are equal, we can devise an algorithm for computing the optimal tree whose time complexity is O (mn), where m and n are the number of links and nodes in the network, respectively. We present a novel integer programming formulation for the general VPN tree computation problem (that is, when ingress and egress bandwidths of VPN endpoints are arbitrary) and develop an algorithm that is based on the primal-dual method. Our experimental results with synthetic network graphs indicate that the VPN trees constructed by our proposed algorithms dramatically reduce bandwidth requirements (in many instances, by more than a factor of 2) compared to scenarios in which Steiner trees are employed to connect VPN endpoints.
Differential Roles of PML Isoforms

The tumor suppressor promyelocytic leukemia (PML) protein is fused to the retinoic acid receptor alpha in patients suffering from acute promyelocytic leukemia (APL). Treatment of APL patients with arsenic trioxide (As2O3) reverses the disease phenotype by a process involving the degradation of the fusion protein via its PML moiety. Several PML isoforms are generated from a single PML gene by alternative splicing. They share the same N-terminal region containing the RBCC/tripartite motif but differ in their C-terminal sequences. Recent studies of all the PML isoforms reveal the specific functions of each. Here, we review the nomenclature and structural organization of the PML isoforms in order to clarify the various designations and classifications found in different databases. The functions of the PML isoforms and their differential roles in antiviral defense also are reviewed. Finally, the key players involved in the degradation of the PML isoforms in response to As2O3 or other inducers are discussed.
Effect of Microcrystalline Cellulose ( MCC ) from Sugar Palm Fibres and Glycerol Addition on Mechanical Properties of Bioplastic from Avocado Seed Starch ( Persea Americana Mill )

The effect of microcrystalline cellulose (MCC) from sugar palm fibers and glycerol addition on mechanical properties of bioplastic from avocado seed (Persea americana mill) were studied. Sugar palm fibers was undergoing alkali treatment, bleaching process, and hydrocloric acid hydrolysis before microcrystalline cellulose can be produced. Degree of crystalinity of MCC were determined by X-Ray Diffraction (XRD), functional group using FT-IR and morphologycal analysis using Scanning Electron Microscope. Mechanical properties of bioplastic were determined by tensile strength, elongation at break, and functional group using FT-IR. Bioplastic was succesfully fabricated through solution casting technique. Bioplastics were prepared from avocado seed starch and reinforced with MCC from sugar palm fibers with composition ratio were 7: 3, 8: 2, and 9: 1 (w/w) and using glycerol as plasticizer with variation of 0,1; 0,2; 0,3 (v/w of starch). MCC dissolved in a solution of NaOH 5% (w/v) before mixed into the plasticized starch. The isolated MCC from sugar palm fibers are rod-like shape with diameter of 5,55-9,44 m and crystallinity 97,5%. From the analysis, the best condition of bioplastics obtained at comparison of mass starch-MCC 7 : 3 and the addition of glycerol 0,2 (v/w) for tensile strength 2,74 MPa and elongation at break 3,16%. The analysis of FT-IR showed the functional groups of bioplastics, which the majority of O-H groups were found at the bioplastics due to addition of MCC that represented substantial hydrogen bonds. c ©2016 The Authors. Published by Academic Fora. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) Peer-review under responsibility of the Scientific & Review committee of ECBA-2016
Tanzania's soil wealth

This paper adopts soil scientific models of soil productivity and degradation in Tanzania into an intertemporal optimisation framework. The farmers choose labour input, capital investment and fertiliser input to maximise soil wealth, i.e., the present value of soil rent. First we focus exclusively on soil mining, considering the nutrient stocks as determinants of land productivity. Next, we focus on soil erosion, and include rooting depth as determinant of land productivity. We compute the soil wealth under the assumption that the opportunity cost of labour is equal to current wages, or alternatively equal to zero. Our estimates suggest that the potential gains from change in agricultural management are considerable. Moreover, the shadow price on root depth and hence the returns to land conservation investments are highly sensitive to our labour market assumptions. We also find that the value of the eroded soil amounts to 12–17 per cent of the value of Hicksian income, and the savings required to maintain consumption amounts to 13–29 per cent of the contribution to GDP.
A probabilistic approach to modeling microstructural variability and fatigue behavior in ASTM F 562 medical grade wire

Several previous studies have demonstrated the importance of constituent inclusion particle distributions on variability in observed fatigue lifetimes. Such models have often concentrated on crack growth behavior in standard test specimens such as single edge notch tension (SENT) geometries. The methodology used here is similar to others in that constituent particles sizes were modelled as initial cracks that were grown to failure using a fracture mechanics approach. Lognormal distributions were fit to inclusion size parameters of 0.178 mm [0.007 in] ASTM F562 alloy medical grade wire. A critical volume approach was used to generate random subsets of inclusion sizes from which particles were chosen with a maximum likelihood of micro-crack generation. These sites were then grown at several stress levels to failure using a plasticity-induced crackclosure model to predict total fatigue life. The resulting lives were found to be in good general agreement with experimentally observed variability in rotary beam fatigue testing.
Zonadhesin Is Essential for Species Specificity of Sperm Adhesion to the Egg Zona Pellucida*

Interaction of rapidly evolving molecules imparts species specificity to sperm-egg recognition in marine invertebrates, but it is unclear whether comparable interactions occur during fertilization in any vertebrate species. In mammals, the sperm acrosomal protein zonadhesin is a rapidly evolving molecule with species-specific binding activity for the egg zona pellucida (ZP). Here we show using null mice produced by targeted disruption of Zan that zonadhesin confers species specificity to sperm-ZP adhesion. Sperm capacitation selectively exposed a partial von Willebrand D domain of mouse zonadhesin on the surface of living, motile cells. Antibodies to the exposed domain inhibited adhesion of wild-type spermatozoa to the mouse ZP but did not inhibit adhesion of spermatozoa lacking zonadhesin. Zan−/− males were fertile, and their spermatozoa readily fertilized mouse eggs in vitro. Remarkably, however, loss of zonadhesin increased adhesion of mouse spermatozoa to pig, cow, and rabbit ZP but not mouse ZP. We conclude that zonadhesin mediates species-specific ZP adhesion, and Zan−/− males are fertile because their spermatozoa retain adhesion capability that is not species-specific. Mammalian sperm-ZP adhesion is therefore molecularly robust, and species-specific egg recognition by a protein in the sperm acrosome is conserved between invertebrates and vertebrates, even though the adhesion molecules themselves are unrelated.