Miracle-dz/UniFAR-FTUs huggingface dataset:
Lattice Simulations of Aggregation Funnels for Protein Folding

A computer model of protein aggregation competing with productive folding is proposed. Our model adapts techniques from lattice Monte Carlo studies of protein folding to the problem of aggregation. However, rather than starting with a single string of residues, we allow independently folding strings to undergo collisions and consider their interactions in different orientations. We first present some background into the nature and significance of protein aggregation and the use of lattice Monte Carlo simulations in understanding other aspects of protein folding. The results of a series of simulation experiments involving simple versions of the model illustrate the importance of considering aggregation in simulations of protein folding and provide some preliminary understanding of the characteristics of the model. Finally, we discuss the value of the model in general and of our particular design decisions and experiments. We conclude that computer simulation techniques developed to study protein folding can provide insights into protein aggregation, and that a better understanding of aggregation may in turn provide new insights into and constraints on the more general protein folding problem.
Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity

Changing a highly conserved amino acid in motif A of any of the four yeast family B DNA polymerases, DNA polymerase α, δ, ɛ or ζ, results in yeast strains with elevated mutation rates. In order to better understand this phenotype, we have performed structure–function studies of homologous mutants of RB69 DNA polymerase (RB69 pol), a structural model for family B members. When Leu415 in RB69 pol is replaced with phenylalanine or glycine, the mutant polymerases retain high-catalytic efficiency for correct nucleotide incorporation, yet have increased error rates due to increased misinsertion, increased mismatch extension and inefficient proofreading. The Leu415Phe mutant also has increased dNTP insertion efficiency opposite a template 8-oxoG and opposite an abasic site. The 2.5 Å crystal structure of a ternary complex of RB69 L415F pol with a correctly base-paired incoming dTTP reveals that the phenylalanine ring is accommodated within a cavity seen in the wild-type enzyme, without steric clash or major change in active site geometry, consistent with retention of high-catalytic efficiency for correct incorporation. In addition, slight structural differences were observed that could be relevant to the reduced fidelity of L415F RB69 pol.
Structured inspections of code

Cleanroom programming and code inspections independently provide evidence that it is more efficient to postpone the testing of code to a later stage than is usually done. This paper argues that an additional gain in quality and efficiency of development can be obtained by structuring inspections by means of an inspection protocol. The written part of such a protocol is prepared by the programmer before the inspection. It is modelled on Floyd's method for the verification of flowcharts. However, the protocol differs from Floyd's method in being applicable in practice. Structured inspections gain this advantage by not attempting to be a proof; they are no more than an articulation of existing forms of inspection. With the usual method of structured programming it may be difficult to prepare the inspection protol. On the other hand, ‘assertion‐driven programming’ (of which an example is included in this paper) not only facilitates protocol preparation, but also the coding itself.
Mechanisms of ATP Release, the Enabling Step in Purinergic Dynamics

The only effective intervention to slow onset and progression of glaucomatous blindness is to lower intraocular pressure (IOP). Among other modulators, adenosine receptors (ARs) exert complex regulation of IOP. Agonists of A3ARs in the ciliary epithelium activate Cl- channels, favoring increased formation of aqueous humor and elevated IOP. In contrast, stimulating A1ARs in the trabecular outflow pathway enhances release of matrix metalloproteinases (MMPs) from trabecular meshwork (TM) cells, reducing resistance to outflow of aqueous humor to lower IOP. These opposing actions are thought to be initiated by cellular release of ATP and its ectoenzymatic conversion to adenosine. This view is now supported by our identification of six ectoATPases in trabecular meshwork (TM) cells and by our observation that external ATP enhances TM-cell secretion of MMPs through ectoenzymatic formation of adenosine. ATP release is enhanced by cell swelling and stretch. Also, enhanced ATP release and downstream MMP secretion is one mediator of the action of actin depolymerization to reduce outflow resistance. Inflow and outflow cells share pannexin-1 and connexin hemichannel pathways for ATP release. However, vesicular release and P2X7 release pathways were functionally limited to inflow and outflow cells, respectively, suggesting that blocking exocytosis might selectively inhibit inflow, lowering IOP.
What ’ s Behind the Inequality We Measure : An Investigation Using Latin American Data

Székely, Miguel. What's behind the inequality we measure : an investigation using Latin American data / by Miguel Székely, Marianne Hilgert. The views and interpretations in this document are those of the authors and should not be attributed to the Inter-American Development Bank, or to any individual acting on its behalf. The Research Department (RES) publishes the Latin American Economic Policies Newsletter, as well as working papers and books, on diverse economic issues. To obtain a complete list of RES publications and read or download them please visit our web site at: Abstract * The use of income distribution indicators in the economics literature has increased considerably in recent years. This work relies on household surveys from 18 LAC countries to take a step back from the use of these indicators, and explore what's behind the numbers, and what information they convey. We find: a) that the way countries rank according to inequality measured in a conventional way is to a large extent an illusion created by differences in characteristics of the data and on the particular ways in which the data is treated; b) Our ideas about the effect of inequality on economic growth are also driven by quality and coverage differences in household surveys and by the way in which the data is treated; c) Standard household surveys in LAC are unable to capture the incomes of the richest sectors of society; so, the inequality we are able to measure is most likely a gross underestimation. Our main conclusion is that there is an important story behind each number. This story influences our judgement about how unequal countries are and about the relation between inequality and other development indicators, but it is seldom told or known. Perhaps other statistics commonly used in economics also have their own interesting story, and it might be worth trying to find out what it is. Ravallion for comments and suggestions. Some parts of Section 4 were used as background research for the Economic and Social Progress Report, 1988 on " Facing Up to Inequality " , by the IDB. The opinions expressed in this paper are the authors' and do not necessarily reflect those of the Inter American Development Bank or its Board of Directors.
Flow cytometric assay for quantifying opsonophagocytosis and killing of Staphylococcus aureus by peripheral blood leukocytes

We describe a novel flow cytometric method for quantifying opsonophagocytosis and killing of Staphylococcus aureus in cell-rich plasma obtained after dextran sedimentation of erythrocytes. To analyze opsonophagocytosis, phagocytes were labeled with a phycoerythrin-conjugated monoclonal antibody and were incubated with viable staphylococci containing carboxyfluorescein as a vital fluorescent dye. Phagocytosing cells assumed a dual, orange-green fluorescence. The relative numbers of bacteria associating with phagocytes could be determined by quantifying the decrease of free green fluorescent particles. A parallel incubation of fluorescent bacteria with unlabeled cell-rich plasma was performed to assess phagocytic killing. Blood cells were lysed with 3-[(3-cholamidopropyl)-dimethyl-ammonio]-1-propanesulfonate. This detergent spared viable bacteria, and residual green fluorescent particles were counted. The decrease in the number of these particles relative to the controls yielded the degree of killing. At bacteria-to-phagocyte ratios of 1:1 and 10:1, approximately 36 and 75% of the phagocytes participated in opsonophagocytosis, respectively. Over 90% of the staphylococci were phagocyte associated after 30 to 60 min. Killing rates were on the order of 66% +/- 12% and 80% +/- 7% after 1 and 2 h of incubation, respectively. These numbers, which were confirmed by colony countings, were significantly lower than those reported in the majority of past reports.
3D object recognition from range images using local feature histograms

The paper explores a view-based approach to recognize free-form objects in range images. We are using a set of local features that are easy to calculate and robust to partial occlusions. By combining those features in a multidimensional histogram, we can obtain highly discriminant classifiers without the need for segmentation. Recognition is performed using either histogram matching or a probabilistic recognition algorithm. We compare the performance of both methods in the presence of occlusions and test the system on a database of almost 2000 full-sphere views of 30 free-form objects. The system achieves a recognition accuracy above 93% on ideal images, and of 89% with 20% occlusion.
The visual status of older persons residing in nursing homes.

OBJECTIVE To characterize habitual visual acuity, contrast sensitivity, spectacle use, and eye care utilization in a large sample of older adults residing in nursing homes. METHODS Of 33 nursing homes identified in Birmingham, Alabama, 17 served as sites. Eligibility criteria included age 55 years or older, English-speaking, and Mini-Mental State Examination score of 13 or higher. Habitual distance and near visual acuity and contrast sensitivity were measured for each eye and binocularly. Residents and a family member/guardian were interviewed about spectacle use and eye care utilization. Medical records provided information on demographics, chronic medical conditions, date of last eye examination, duration of residence in the nursing home, and health insurance. RESULTS Of 380 enrollees, 57% had distance visual acuity in the better eye worse than 20/40; 10% had visual acuity of 20/200 or worse. Near visual acuity was slightly worse on average by a line than distance acuity. Three-fourths of residents had abnormal binocular contrast sensitivity. The medical record had no record of or reference to an eye examination for 66% of enrollees despite 90% having health insurance. CONCLUSION The high rate of visual impairment in nursing homes underscores the need to understand its causes and to evaluate interventions to address this public health challenge.
Translation of Einstein's Attempt of a Unified Field Theory with Teleparallelism

We present the first English translation of Einstein's original papers related to the teleparallel ('absolute parallelism', 'distant parallelism' and the German 'Fernparallelismus' are synonyms) attempt of an unified field theory of gravitation and electromagnetism. Our collection contains the summarizing paper in Math. Annal. 102 (1930) pp. 685-697 and 2 reports published in 'Sitzungsberichte der Preussischen Akademie der Wissenschaften' on June 7th, 1928 (pp. 217-221), June 14th, 1928 (pp. 224-227) and a precursor report (July 9th, 1925 pp. 414-419). To ease understanding, literature on tensor analysis is quoted in the footnotes.
Effect of exercise protocol on deoxy[Hb + Mb]: incremental step versus ramp exercise.

PURPOSE The aim of the present study was to investigate whether the sigmoid pattern of deoxy[Hb + Mb] during incremental exercise is specific to non-steady-state conditions. METHODS Ten highly trained cyclists performed an incremental step (40 W x 3 min(-1)) and ramp (35 W x min(-1)) exercise. Deoxy[Hb + Mb] was measured at the distal and proximal sites of the musculus vastus lateralis throughout the exercises using near-infrared spectroscopy. Deoxy[Hb + Mb] was set out as a function of work rate (% peak power), and using curve-fitting techniques, the best-fitting model was determined. RESULTS These procedures showed that the sigmoid pattern also provided the best fit for the pattern of deoxy[Hb + Mb] in the step exercise. Furthermore, it was observed that the sigmoid model was similar for the ramp (d = 6.9% +/- 1.1% and 6.9% +/- 1.4% x %(-1) peak power; c/d = 52.1% +/- 3.8% and 52.1% +/- 4.5% peak power, for the proximal and distal measurement sites, respectively) and the step exercise (d = 7.4% +/- 1.5% and 6.4% +/- 1.5% x %(-1) peak power; c/d = 52.3% +/- 6.0% and 52.5% +/- 4.2% peak power, for the proximal and distal measurement sites, respectively). The pattern of deoxy[Hb + Mb] was not influenced by measurement site. CONCLUSIONS From the present study, it can be concluded that the sigmoid pattern of deoxy[Hb + Mb] during incremental exercise is not specific to non-steady-state conditions. It was hypothesized that this pattern is an expression of a nonlinear Q x m/V x O2m relationship, related to changes in muscle fiber-type recruitment.
Discovery and Validation of a Prostate Cancer Genomic Classifier that Predicts Early Metastasis Following Radical Prostatectomy

Purpose Clinicopathologic features and biochemical recurrence are sensitive, but not specific, predictors of metastatic disease and lethal prostate cancer. We hypothesize that a genomic expression signature detected in the primary tumor represents true biological potential of aggressive disease and provides improved prediction of early prostate cancer metastasis. Methods A nested case-control design was used to select 639 patients from the Mayo Clinic tumor registry who underwent radical prostatectomy between 1987 and 2001. A genomic classifier (GC) was developed by modeling differential RNA expression using 1.4 million feature high-density expression arrays of men enriched for rising PSA after prostatectomy, including 213 who experienced early clinical metastasis after biochemical recurrence. A training set was used to develop a random forest classifier of 22 markers to predict for cases - men with early clinical metastasis after rising PSA. Performance of GC was compared to prognostic factors such as Gleason score and previous gene expression signatures in a withheld validation set. Results Expression profiles were generated from 545 unique patient samples, with median follow-up of 16.9 years. GC achieved an area under the receiver operating characteristic curve of 0.75 (0.67–0.83) in validation, outperforming clinical variables and gene signatures. GC was the only significant prognostic factor in multivariable analyses. Within Gleason score groups, cases with high GC scores experienced earlier death from prostate cancer and reduced overall survival. The markers in the classifier were found to be associated with a number of key biological processes in prostate cancer metastatic disease progression. Conclusion A genomic classifier was developed and validated in a large patient cohort enriched with prostate cancer metastasis patients and a rising PSA that went on to experience metastatic disease. This early metastasis prediction model based on genomic expression in the primary tumor may be useful for identification of aggressive prostate cancer.
A simple transmit diversity technique for wireless communications

This paper presents a simple two-branch transmit diversity scheme. Using two transmit antennas and one receive antenna the scheme provides the same diversity order as maximal-ratio receiver combining (MRRC) with one transmit antenna, and two receive antennas. It is also shown that the scheme may easily be generalized to two transmit antennas and M receive antennas to provide a diversity order of 2M. The new scheme does not require any bandwidth expansion or any feedback from the receiver to the transmitter and its computation complexity is similar to MRRC.
Survival and Competitiveness of Bradyrhizobium japonicum Strains 20 Years after Introduction into Field Locations in Poland

ABSTRACT It was previously demonstrated that there are no indigenous strains of Bradyrhizobium japonicum forming nitrogen-fixing root nodule symbioses with soybean plants in arable field soils in Poland. However, bacteria currently classified within this species are present (together with Bradyrhizobium canariense) as indigenous populations of strains specific for nodulation of legumes in the Genisteae tribe. These rhizobia, infecting legumes such as lupins, are well established in Polish soils. The studies described here were based on soybean nodulation field experiments, established at the Poznań University of Life Sciences Experiment Station in Gorzyń, Poland, and initiated in the spring of 1994. Long-term research was then conducted in order to study the relation between B. japonicum USDA 110 and USDA 123, introduced together into the same location, where no soybean rhizobia were earlier detected, and nodulation and competitive success were followed over time. Here we report the extra-long-term saprophytic survival of B. japonicum strains nodulating soybeans that were introduced as inoculants 20 years earlier and where soybeans were not grown for the next 17 years. The strains remained viable and symbiotically competent, and molecular and immunochemical methods showed that the strains were undistinguishable from the original inoculum strains USDA 110 and USDA 123. We also show that the strains had balanced numbers and their mobility in soil was low. To our knowledge, this is the first report showing the extra-long-term persistence of soybean-nodulating strains introduced into Polish soils and the first analyzing the long-term competitive relations of USDA 110 and USDA 123 after the two strains, neither of which was native, were introduced into the environment almost 2 decades ago.
Proteomic analysis reveals a virtually complete set of proteins for translation and energy generation in elementary bodies of the amoeba symbiont Protochlamydia amoebophila

Chlamydiae belong to the most successful intracellular bacterial pathogens. They display a complex developmental cycle and an extremely broad host spectrum ranging from vertebrates to protozoa. The family Chlamydiaceae comprises exclusively well‐known pathogens of humans and animals, whereas the members of its sister group, the Parachlamydiaceae, naturally occur as symbionts of free‐living amoebae. Comparative analysis of these two groups provides valuable insights into chlamydial evolution and mechanisms for microbe–host interaction. Based on the complete genome sequence of the Acanthamoeba spp. symbiont Protochlamydia amoebophila UWE25, we performed the first detailed proteome analysis of the infectious stage of a symbiotic chlamydia. A 2‐D reference proteome map was established and the analysis was extensively complemented by shotgun proteomics. In total, 472 proteins were identified, which represent 23.2% of all encoded proteins. These cover a wide range of functional categories, including typical house‐keeping proteins, but also putative virulence‐associated proteins. A number of proteins that are not encoded in genomes of Chlamydiaceae were observed and the expression of 162 proteins classified as hypothetical or unknown proteins could be demonstrated. Our findings indicate that P. amoebophila exploits its additional genetic repertoire (compared with the Chlamydiaceae), and that its elementary bodies are remarkably well equipped with proteins involved in transcription, translation, and energy generation.
Statistical Modeling of Carbonation in Concrete Incorporating Recycled Aggregates

Durability and recycling are two major concerns in the construction industry. Concrete carbonation may impair reinforced concrete durability as it favors the onset of reinforcement corrosion. The use of recycled aggregates, as a replacement for natural aggregates, in construction applications is a feasible way of recycling given materials from construction and demolition waste. The aim of this study is to quantify the contribution of potential conditioning factors to the carbonation rate of concrete incorporating recycled aggregates. For this purpose, a multiple linear regression technique was used, considering the mix design characteristics, environmental conditions, and recycled aggregates’ properties as explanatory variables, capable of predicting the coefficient of carbonation. The investigation was founded on ample experimental data, collated from several studies. This study proposes a general model, in which the carbonation in concrete depends on the 28-day compressive strength, clinker content, environment’s CO₂ content, and aggregates’ equivalent water absorption. The models are statistically significant, with determination coefficients suggesting high correlation between the coefficients of accelerated carbonation of concrete in the experimental data and values predicted by the proposed models.
ACTH Action on StAR Biology

Adrenocorticotropin hormone (ACTH) produced by the anterior pituitary stimulates glucocorticoid synthesis by the adrenal cortex. The first step in glucocorticoid synthesis is the delivery of cholesterol to the mitochondrial matrix where the first enzymatic reaction in the steroid hormone biosynthetic pathway occurs. A key response of adrenal cells to ACTH is activation of the cAMP-protein kinase A (PKA) signaling pathway. PKA activation results in an acute increase in expression and function of the Steroidogenic Acute Regulatory protein (StAR). StAR plays an essential role in steroidogenesis- it controls the hormone-dependent movement of cholesterol across the mitochondrial membranes. Currently StAR's mechanism of action remains a major unanswered question in the field. However, some insight may be gained from understanding the mechanism(s) controlling the PKA-dependent phosphorylation of StAR at S194/195 (mouse/human StAR), a modification that is required for function. This mini-review provides a background on StAR's biology with a focus on StAR phosphorylation. The model for StAR translation and phosphorylation at the outer mitochondrial membrane, the location for StAR function, is presented to highlight a unifying theme emerging from diverse studies.