Miracle-dz/UniFAR-FTUs huggingface dataset:
An Integrated Framework Advancing Membrane Protein Modeling and Design

Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design.
Sequential Treatment with Basic Fibroblast Growth Factor and Parathyroid Hormone Restores Lost Cancellous Bone Mass and Strength in the Proximal Tibia of Aged Ovariectomized Rats

This study was designed to determine whether sequential treatment with basic fibroblast growth factor (bFGF) and parathyroid hormone (PTH) can restore lost cancellous bone mass and strength at a severely osteopenic skeletal site in aged ovariectomized (OVX) rats. Female Sprague‐Dawley rats were subjected to sham surgery or ovariectomy at 3 months of age and maintained untreated for the first year after surgery. At 15 months of age, groups of baseline control and OVX rats were killed and catheters were inserted in the jugular veins of all remaining rats. Two groups of OVX rats were injected intravenously (iv) daily with bFGF for 14 days at a dose of 200 μg/kg body weight. At the end of bFGF treatment, one group was killed whereas the other group was subjected to 8 weeks of treatment with synthetic human PTH 1‐34 [hPTH(1‐34)] consisting of subcutaneous (sc) injections 5 days/week at a dose of 80 μg/kg. Another group of OVX rats was treated iv with vehicle for 2 weeks followed by treatment with PTH alone for 8 weeks. Other groups of sham‐operated control rats and OVX rats were treated iv and sc with vehicle alone. The right proximal tibia from each rat was processed undecalcified for quantitative bone histomorphometry and the left proximal tibia was subjected to biomechanical testing. Baseline and vehicle‐treated OVX rats were severely osteopenic because their tibial cancellous bone volumes were less than 5% compared with mean values of 20.3% and 15.0% in baseline and vehicle‐treated control rats, respectively. Treatment of OVX rats for 2 weeks with bFGF alone did not significantly increase tibial cancellous bone volume but induced marked increases in osteoid volume, osteoblast surface, and osteoid surface. Sequential treatment of aged OVX rats with bFGF and PTH increased tibial cancellous bone volume (15.1%) and load to failure to at least the level of vehicle‐treated control rats. Tibial cancellous bone volume (10.8%) and load to failure also were significantly increased by treatment with PTH alone, and these variables were not significantly different from those of OVX rats treated with bFGF + PTH. However, tibial ash density was significantly greater in OVX rats treated sequentially with bFGF and PTH compared with OVX rats treated with PTH alone. Our findings suggest that sequential treatment with bFGF and PTH may be useful for restoration of lost cancellous bone in the severely osteopenic, estrogen‐deplete skeleton, but it cannot be concluded with certainty that this sequential treatment has a greater bone restorative effect than treatment with PTH alone.
Maternal antibodies to dietary antigens and risk for nonaffective psychosis in offspring.

OBJECTIVE The authors analyzed archival dried blood spots obtained from newborns to assess whether levels of immunoglobulin G (IgG) directed at dietary antigens were associated with a later diagnosis of a nonaffective psychotic disorder. METHOD The study population consisted of individuals born in Sweden between 1975 and 1985 with verified register-based diagnoses of nonaffective psychoses made between 1987 and 2003 and comparison subjects matched on sex, date of birth, birth hospital, and municipality. A total of 211 case subjects and 553 comparison subjects consented to participate in the study. Data on factors associated with maternal status, pregnancy, and delivery were extracted from the Swedish Medical Birth Register. Levels of IgG directed at gliadin (a component of gluten) and casein (a milk protein) were analyzed in eluates from dried blood spots by enzyme-linked immunosorbent assay. Odds ratios were calculated for levels of IgG directed at gliadin or casein for nonaffective psychosis. RESULTS Levels of anti-gliadin IgG (but not anti-casein IgG) above the 90th percentile of levels observed among comparison subjects were associated with nonaffective psychosis (odds ratio=1.7, 95% CI=1.1-2.8). This association was not confounded by differences in maternal age, immigrant status, or mode of delivery. Similarly, gestational age at birth, ponderal index, and birth weight were not related to maternal levels of anti-gliadin IgG. CONCLUSIONS High levels of anti-gliadin IgG in the maternal circulation are associated with an elevated risk for the development of a nonaffective psychosis in offspring. Research is needed to identify the mechanisms underlying this association in order to develop preventive strategies.
An Investigation into the Cognition Behind Spontaneous String Pulling in New Caledonian Crows

The ability of some bird species to pull up meat hung on a string is a famous example of spontaneous animal problem solving. The “insight” hypothesis claims that this complex behaviour is based on cognitive abilities such as mental scenario building and imagination. An operant conditioning account, in contrast, would claim that this spontaneity is due to each action in string pulling being reinforced by the meat moving closer and remaining closer to the bird on the perch. We presented experienced and naïve New Caledonian crows with a novel, visually restricted string-pulling problem that reduced the quality of visual feedback during string pulling. Experienced crows solved this problem with reduced efficiency and increased errors compared to their performance in standard string pulling. Naïve crows either failed or solved the problem by trial and error learning. However, when visual feedback was available via a mirror mounted next to the apparatus, two naïve crows were able to perform at the same level as the experienced group. Our results raise the possibility that spontaneous string pulling in New Caledonian crows may not be based on insight but on operant conditioning mediated by a perceptual-motor feedback cycle.
Use of a parallel artificial membrane system to evaluate passive absorption and elimination in small fish

A parallel artificial lipid membrane system was developed to mimic passive mass transfer of hydrophobic organic chemicals in fish. In this physical model system, a membrane filter–supported lipid bilayer separates two aqueous phases that represent the external and internal aqueous environments of fish. To predict bioconcentration kinetics in small fish with this system, literature absorption and elimination rates were analyzed with an allometric diffusion model to quantify the mass transfer resistances in the aqueous and lipid phases of fish. The effect of the aqueous phase mass transfer resistance was controlled by adjusting stirring intensity to mimic bioconcentration rates in small fish. Twenty‐three simple aromatic hydrocarbons were chosen as model compounds for purposes of evaluation. For most of the selected chemicals, literature absorption/elimination rates fall into the range predicted from measured membrane permeabilities and elimination rates of the selected chemicals determined by the diffusion model system.
Multiple molecular evidences for a living mammalian fossil

Laonastes aenigmamus is an enigmatic rodent first described in 2005. Molecular and morphological data suggested that it is the sole representative of a new mammalian family, the Laonastidae, and a member of the Hystricognathi. However, the validity of this family is controversial because fossil-based phylogenetic analyses suggest that Laonastes is a surviving member of the Diatomyidae, a family considered to have been extinct for 11 million years. According to these data, Laonastes and Diatomyidae are the sister clade of extant Ctenodactylidae (i.e., gundies) and do not belong to the Hystricognathi. To solve the phylogenetic position of Laonastes, we conducted a large-scale molecular phylogeny of rodents. The analysis includes representatives of all major rodent taxonomic groups and was based on 5.5 kb of sequence data from four nuclear and two mitochondrial genes. To further validate the obtained results, a short interspersed element insertion analysis including 11 informative loci was also performed. Our molecular data based on sequence and short interspersed element analyses unambiguously placed Laonastes as a sister clade of gundies. All alternative hypotheses were significantly rejected based on Shimodaira–Hasegawa tests, supporting the idea that Laonastes does not belong to the Hystricognathi. Molecular dating analysis also supports an ancient divergence, ≈44 Mya ago, between Ctenodactylidae and Laonastes. These combined analyses support the hypothesis that Laonastes is indeed a living fossil. Protection of this surviving species would conserve an ancient mammalian family.
Multiple ant-colony optimization for network routing

An ANT is a mobile agent that is capable of solving various kinds of routing and congestion problems in computer networking by continuously modifying routing tables in response to congestion. In a distributed problem solving paradigm, a society of ANTs (each contributing some information) collaborate to solve a larger problem. In recent years, ant-based algorithms were used to solve classical routing problems such as: traveling salesman problem, vehicle routing problem, quadratic assignment problem, connection-oriented/connectionless routing, sequential ordering, graph coloring and shortest common supersequence. This paper introduces the general idea of Ant-based algorithms with a focus on ant colony optimization (ACO), and their features, strengths, weaknesses and applications in network routing. The contribution of this paper is the proposal of a multiple ant-colony optimization (MACO) approach for network routing.
Pattern and Predictors of Unmet Supportive Care Needs in Cancer Patients

The incidence of cancers is increasing and this is associated with an increase in the burden of the disease. Patients with cancer have to deal with reduced physical functioning, emotional instability, difficulty in concentrating, and an overall diminished feeling of well-being. This creates deficits that have not been well catered for by traditional cancer care, leading to an overall dissatisfaction with care and a reduced quality of life. This review aims at assessing the pattern of unmet needs in cancer patients and to provide information as to the factors that influence the perception of unmet needs. Studies directly focused on unmet needs in cancer patients which were retrieved from Medical Literature Analysis and Retrieval System Online (MEDLINE), Public/Publisher Medline (PubMed), PsychINFO, Excerpta Medica database (EMBASE), and Google Scholar; from the earliest records till 2016. Unmet needs in cancer patients have been measured with a wide variety of tools, with the supportive care needs survey (SCNS) being the most commonly used as a result of its strong psychometric properties, ease of use, responsiveness, and its coverage of the major domains of unmet needs. The most common unmet needs were in the domains of health system and information, psychological, and physical and daily living. These needs are influenced by sociodemographic factors such as age, sex, marital status, income level; and clinical factors such as location of cancer, stage of disease, and tumor size. It is clear that cancer patients experience a wide range of unmet supportive needs, for which solutions need to be devised in order to improve the supportive care services for these patients and their overall quality of life.
Mohs's Hardness Scale - A Physical Interpretation

The Mohs hardness scale consists of ten minerals arranged in increasing order of hardness such that each mineral will scratch the one on the scale below it, but will not scratch the one above it. Although these minerals are generally considered to be brittle, experiments show that under local indentation and during sliding their behaviour is primarily determined by the plastic properties of the minerals. This suggests that there should be some relation between the Mohs hardness and the indentation hardness of the minerals. Experiments with metals show that in general a metal surface of indentation hardness Hs will be scratched by a point of hardness Hp if Hp gt-or-equal, slanted 1.2 Hs. Thus a scratch hardness scale can be constructed in which each standard has an indentation hardness at least 1.2 times greater than the preceding standard. The scratch hardness number is then proportional to the logarithm of the indentation hardness. Excluding diamond, which is anomalous, this type of relation is found to apply to the Mohs standards, and it is found that each standard is approximately 60% harder than the preceding one.
Viscosity and Crystallization Behavior of F-free Mold Flux for Casting Medium Carbon Steels

Viscosity and crystallization are essential properties to characterize the lubrication and heat transfer performances of mold flux. Therefore, in this paper, the viscosity and crystallization behaviors of conventional F-containing commercial mold flux and newly designed F-free mold fluxes were investigated by using rotating cylinder method and Single/Double Hot Thermocouple Technique (SHTT/DHTT). Results shows that the viscosities of designed F-free mold fluxes are close to the F-containing mold flux; and the crystallization temperatures of F-free mold fluxes increases with the increase of basicity and Na2O/Li2O content; while it decreases with the increase of cooling rate and the addition of B2O3. The final steady state structure of F-free mold fluxes during the DHTT tests shows it is composed of a major crystalline and a thin liquid layer (5.42–7.2%) without glass phase. The results of XRD indicate that the main crystalline phases formed in designed F-free mold fluxes were calcium borosilicate (Ca11Si4B2O22) and calcium magnesium silicate (Ca14Mg2(SiO4)8. Through the comprehensive comparison, the designed F-free mold fluxes flux Sample E (Basicity 1.15, Na2O 7.92, Li2O 1.97 and B2O3 5.98) has the closest performances to the benchmark conventional mold flux Sample A.
What Are Analytic Narratives?

The recently born expression "analytic narratives" refers to studies that have appeared at the boundaries of history, political science, and economics. These studies purport to explain specific historical events by combining the usual narrative way of historians with the analytic tools that economists and political scientists find in rational choice theory. Game theory is prominent among these tools. The paper explains what analytic narratives are by sampling from the eponymous book Analytic Narratives by Bates, Greif, Levi, Rosenthal, and Weingast (1998) and covering one outside study by Mongin (2008). It first evaluates the explanatory performance of the new genre, using some philosophy of historical explanation and then checks its discursive consistency, using some narratology. The paper concludes that analytic narratives can usefully complement standard narratives in historical explanation, provided they specialize in the gaps that these narratives reveal and that they are discursively consistent, despite the tension that combining a formal model with a narration creates. Two expository modes, called alternation and local supplementation, emerge from the discussion as the most appropriate ones to resolve this tension
Assessing Piketty’s laws of capitalism

This paper tests Piketty's predictions that in the long run (i) the capital-income ratio, K-Y, is driven by the ratio between the rates of saving and income growth, s and g; and that (ii) the capital share of income responds to variations in the s-g ratio, along with the rate of return on capital, r. We assess the two predictions using both Piketty and Zucman's (2014) original data and a new long historical dataset covering 21 OECD countries. Our findings corroborate Piketty’s theory in the very long run (1870-2010), whilst evidence for the latest decades is less robust (1970-2010).
Clinical value of the cultural formulation interview in Pune, India

Context: Development of the cultural formulation interview (CFI) in DSM-5 required validation for cross-cultural and global use. Aims: To assess the overall value (OV) of CFI in the domains of feasibility, acceptability, and utility from the vantage points of clinician-interviewers, patients and accompanying relatives. Settings and Design: We conducted cross-sectional semi-structured debriefing interviews in a psychiatric outpatient clinic of a general hospital. Materials and Methods: We debriefed 36 patients, 12 relatives and eight interviewing clinicians following the audio-recorded CFI. We transformed their Likert scale responses into ordinal values – positive for agreement and negative for disagreement (range +2 to −2). Statistical Analysis: We compared mean ratings of patients, relatives and clinician-interviewers using nonparametric tests. Clinician-wise grouping of patients enabled assessment of clinician effects, inasmuch as patients were randomly interviewed by eight clinicians. We assessed the influence of the presence of relatives, clinical diagnosis and interview characteristics by comparing means. Patient and clinician background characteristics were also compared. Results: Patients, relatives and clinicians rated the CFI positively with few differences among them. Patients with serious mental disorders gave lower ratings. Rating of OV was lower for patients and clinicians when relatives were present. Clinician effects were minimal. Clinicians experienced with culturally diverse patients rated the CFI more positively. Narratives clarified the rationale for ratings. Conclusions: Though developed for the American DSM-5, the CFI was valued by clinicians, patients and relatives in out-patient psychiatric assessment in urban Pune, India. Though relatives may add information and other value, their presence in the interview may impose additional demands on clinicians. Our findings contribute to cross-cultural evaluation of the CFI.
Carotenoid Biosynthesis in Cyanobacteria: Structural and Evolutionary Scenarios Based on Comparative Genomics

Carotenoids are widely distributed pigments in nature and their biosynthetic pathway has been extensively studied in various organisms. The recent access to the overwhelming amount genomic data of cyanobacteria has given birth to a novel approach called comparative genomics. The putative enzymes involved in the carotenoid biosynthesis among the cyanobacteria were determined by similarity-based tools. The reconstruction of biosynthetic pathway was based on the related enzymes. It is interesting to find that nearly all the cyanobacteria share quite similar pathway to synthesize β-carotene except for Gloeobacter violaceus PCC 7421. The enzymes, crtE-B-P-Qb-L, involved in the upstream pathway are more conserved than the subsequent ones (crtW-R). In addition, many carotenoid synthesis enzymes exhibit diversity in structure and function. Such examples in the families of ζ –carotene desaturase, lycopene cylases and carotene ketolases were described in this article. When we mapped these crt genes to the cyanobacterial genomes, the crt genes showed great structural variation among species. All of them are dispersed on the whole chromosome in contrast to the linear adjacent distribution of the crt gene cluster in other eubacteria. Moreover, in unicellular cyanobacteria, each step of the carotenogenic pathway is usually catalyzed by one gene product, whereas multiple ketolase genes are found in filamentous cyanobacteria. Such increased numbers of crt genes and their correlation to the ecological adaptation were carefully discussed.
Subcutaneous Panniculitis-Like T Cell Lymphoma Mimicking Early-Onset Nodular Panniculitis

Patient: Male, 24 Final Diagnosis: Subcutaneous panniculitis-like T-cell lymphoma Symptoms: Fever • skin nodules Medication: — Clinical Procedure: Skin biopsy • PET-CT Specialty: Hematology Objective: Rare disease Background: Subcutaneous panniculitis-like T cell lymphoma is a very uncommon subtype of cutaneous T cell lymphoma. The manifestations of this rare disease are atypical at onset, and may mimic some rheumatic or dermatologic diseases, which causes the delay of diagnosis and treatment. Case Report: We report a 24-year-old man suffering from intermittent fever and skin nodules on the left anterior chest wall, who was initially misdiagnosed with nodular panniculitis and finally diagnosed with subcutaneous panniculitis-like T cell lymphoma through repeat examination of biopsy of the skin nodule. Positron emission tomography revealed extracutaneous adipose tissue involvement. Subsequently, hemophagocytic syndrome occurred while under a conventional dose of glucocorticoid, but remission was induced by treatment with cyclosporine A and high doses of dexamethasone. Conclusions: In order to avoid the delay diagnosis and inappropriate treatment of subcutaneous panniculitis-like T cell lymphoma, in addition to a thorough physical examination, PET-CT and disease-specific pathologic, immunophenotypic, and T cell receptor tests of the skin biopsy should be performed. Extracutaneous involvement, especially hemophagocytic syndrome, indicated worse prognosis. Even so, cyclosporine A plus high-dose corticosteroid could be an option of treatment.
Completing Low-Rank Matrices With Corrupted Samples From Few Coefficients in General Basis

Subspace recovery from the corrupted and missing data is crucial for various applications in signal processing and information theory. To complete missing values and detect column corruptions, the existing robust matrix completion (MC) methods mostly concentrate on recovering a low-rank matrix from a few corrupted coefficients with respect to standard basis, which, however, does not apply to more general basis, e.g., Fourier basis. In this paper, we prove that the range space of an m × n matrix with rank r can be exactly recovered from a few coefficients with respect to general basis, though r and the number of corrupted samples are both as high as O(min{m, n}/ log3(m + n)). Our model covers the previous ones as special cases, and robust MC can recover the intrinsic matrix with a higher rank. Moreover, we suggest a universal choice of the regularization parameter, which is λ = 1/√log n. By our ℓ2,1 filtering algorithm, which has theoretical guarantees, we can further reduce the computational cost of our model. As an application, we also find that the solutions to extended robust low-rank representation and to our extended robust MC are mutually expressible, so both our theory and algorithm can be applied to the subspace clustering problem with missing values under certain conditions. The experiments verify our theories.