Miracle-dz/UniFAR-FTUs huggingface dataset:
Clonal B cell populations in a minority of patients with Hashimoto’s thyroiditis

Background: Hashimoto’s thyroiditis (HT) is a risk factor for thyroid lymphoma, and clonal B cell populations in HT support this link. The literature on B cell clonality in HT is controversial. Aims: To identify clonal B cell populations in HT and to assess their usefulness in differentiating HT from mucosa associated lymphoid tissue (MALT) lymphoma and predicting future development of lymphoma. Methods: DNA from formalin fixed, paraffin wax embedded blocks of thyroid specimens from 10 patients with HT and two thyroid MALT lymphomas was analysed for B cell clonality by seminested polymerase chain reaction (PCR) using FRIII/LJH and FRIII/VLJH primers to amplify the IgH gene VDJ region. In one case, PCR products were sequenced. Immunohistochemistry was performed by labelled streptavidin–biotin technique using antibodies to: CD45, CD45RO, CD3, CD20, and cytokeratin. Results: The histopathological and clinical findings were characteristic of HT. Clonal bands were seen in three and a polyclonal smear pattern was seen in seven cases. The clonal bands in HT were associated with a background smear, and could not be reproduced from other blocks from the same case or from deeper sections of the same block. The clonal bands in thyroid lymphomas were not associated with a background smear and were reproducible. None of the patients with clonal B cells has developed malignant lymphoma during a follow up of 10–13 years. Conclusions: B cell clonal bands in HT have different features from those in lymphoma (non-pure and non-reproducible) and do not predict future development of lymphoma.
Urinary α1-Antichymotrypsin: A Biomarker of Prion Infection

The occurrence of blood-borne prion transmission incidents calls for identification of potential prion carriers. However, current methods for intravital diagnosis of prion disease rely on invasive tissue biopsies and are unsuitable for large-scale screening. Sensitive biomarkers may help meeting this need. Here we scanned the genome for transcripts elevated upon prion infection and encoding secreted proteins. We found that α1-antichymotrypsin (α1-ACT) was highly upregulated in brains of scrapie-infected mice. Furthermore, α1-ACT levels were dramatically increased in urine of patients suffering from sporadic Creutzfeldt-Jakob disease, and increased progressively throughout the disease. Increased α1-ACT excretion was also found in cases of natural prion disease of animals. Therefore measurement of urinary α1-ACT levels may be useful for monitoring the efficacy of therapeutic regimens for prion disease, and possibly also for deferring blood and organ donors that may be at risk of transmitting prion infections.
Barriers to prompt and effective treatment of malaria in northern Sri Lanka

BACKGROUND For the past 18 years, northern Sri Lanka has been affected by armed ethnic conflict. This has had a heavy impact on displacement of civilians, health delivery services, number of health professionals in the area and infrastructure. The north of Sri Lanka has a severe malaria burden, with less than 5% of the national population suffering 34% of reported cases. Health care providers investigated treatment‐seeking behaviour and levels of treatment failure believed to be the result of lack of adherence to treatment.
Physical layer security for optical attocell networks

In this paper, physical layer security for optical attocell networks is studied. The secrecy throughput of four different types of optical attocell deployment, hexagonal (HEX), square, poisson point process (PPP) and hard-core point process (HCPP) are compared. In order to improve system confidentiality, angle diversity transmitters are implemented in optical attocell networks. An angle diversity transmitter usually consists of multiple narrow-beam light-emitting diode (LED) elements with different orientations. Angle diversity transmitters are very suitable for secure transmission since data transmission via narrow light beams can effectively avoid the leakage of messages. Results show that HEX deployment performs the best in terms of secrecy throughput while PPP deployment performs the worst. With the use of angle diversity transmitters, secrecy throughput of optical attocell networks can be significantly improved. Compared with single-element transmitter, over 6 times secrecy throughput improvement can be obtained by using 18-element angle diversity transmitter.
Publisher Accessed Terms of Use Detailed Terms On-line Embeddings

The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Abstract We initiate the study of on-line metric embeddings. In such an embedding we are given a sequence of n points X = x 1 ,. , x n one by one, from a metric space M = (X, D). Our goal is to compute a low-distortion embedding of M into some host space, which has to be constructed in an on-line fashion, so that the image of each x i depends only on x 1 ,. , x i. We prove several results translating existing embeddings to the on-line setting, for the case of embedding into p spaces, and into distributions over ultrametrics.
Heirs of box types in polynomially bounded structures

Abstract A box type is an n-type of an o-minimal structure which is uniquely determined by the projections to the coordinate axes. We characterize heirs of box types of a polynomially bounded o-minimal structure M. From this, we deduce various structure theorems for subsets of Mk, definable in the expansion of M by all convex subsets of the line. We show that after naming constants, is model complete provided M is model complete.
Biological Identifications Through DNA Barcodes

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon ‘barcodes’. It was established previously that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. A new tools were developed recently to be complementary markers for (COI) DNA barcoding.
Evaluation of human immunodeficiency virus seroprevalence in population surveys using pooled sera

The pooling of individual serum samples to determine human immunodeficiency virus (HIV) seropositivity was examined to assess whether testing pooled sera was technically feasible, cost-effective, and accurate for estimating seroprevalence in large population surveys. The sensitivities and specificities of three commercially available HIV enzyme-linked immunosorbent assay (ELISA) kits were tested using 65 serum pools of 15 individual serum samples each (975 total serum samples) at two different dilutions. With pooled sera, the Organon Teknika Bio-EnzaBead ELISA at half the dilution recommended by the manufacturer showed the best agreement with ELISA and Western blot results of individual sera. In subsequently testing 92 pools, each containing 15 individual serum samples from a population of American patients attending a sexually transmitted diseases clinic, the estimated seroprevalence was 5.27 compared with 4.93% in a test of 1,380 individual serum samples and 5.19% in a test of 4,028 individual serum samples from the same population. In an evaluation of 1,380 African patients using 10 serum samples per pool, the estimated seroprevalence was 5.79 compared with 6.16% in a test of individual sera. These results indicate that ELISA testing with pooled sera is highly sensitive and specific and appears to be a cost-effective means for estimating HIV seroprevalence in large population-based surveys.
Information Flows in Capacitated Supply Chains with Fixed Ordering Costs

Many organizations have only recently recognized that sharing information with other members in their supply chain can lead to signficant reduction in the total costs.Usually these information flows are incorporated into existing operating policies at the various parties.In this paper we argue that, in some cases, it may be necessary to change the way the supply chain is managed to make complete use of the information flows. We support this argument by analyzing a supply chain containing a capacitated supplier and a retailer facing i.i. d. demands. In addition there are fixed ordering costs between the retailer and the supplier.In this setting, we consider two models: 1 the retailer is using the optimal s,S policy and providing the supplier information about her inventory levels; and 2 the retailer, still sharing information on her inventory levels, orders in a period only if by the previous period the cumulative end-customer demand since she last ordered was greater than δ. Thus, in Model 1, information sharing is used to supplement existing policies; while, in Model 2, we have redefined operating policies to make better use of the information flows. We will show, via a detailed computational study, that the total supply chain costs of Model 2 are 10.4% lower, on the average, than that of Model 1. We noticed that this reduction in costs is higher at higher capacities, higher supplier penalty costs, lower retailer penalty costs, moderate values of set-up cost, and at lower end-customer demand variances.
Surveillance systems for sexually transmitted infections: a global review

Purpose of review Sexually transmitted infections (STIs) continue to exert a substantial public health burden globally but surveillance remains a challenge, especially in the developing world. We reviewed STI surveillance systems in various regions globally and used available data to provide an overview of recent trends in STI epidemiology. Recent findings STI surveillance systems in the developing world are often limited and restricted to ad hoc cross-sectional surveys; however, available data suggest that these areas are disproportionately affected by STIs, with a higher burden in marginalized groups such as sex workers. Developed countries typically have established surveillance systems. Recent reports suggest many of these countries are experiencing rising diagnoses of STIs in men who have sex with men (MSM) and an increasing contribution of HIV-positive MSM to STI epidemics. Summary There is considerable variability in the surveillance for STIs globally, ranging from active or passive, to sentinel, laboratory or clinic-based systems. Given different levels of resources and patterns of healthcare provision, it is difficult to compare surveillance data across regions; however, available data suggest that considerable inequality in STI burden exists. In resource-limited settings, syndromic surveillance with periodic laboratory assessments is recommended to monitor trends in STIs.
A Novel Approach to Ring Resonator Theory Involving Even and Odd Mode Analysis

This paper presents a novel theoretical approach to the analysis of a ring resonator consisting of an edge-fed circular microstrip of arbitrary width on a substrate over a ground plane; the analysis takes into account the existing coupling between the two halves of the ring. The proposed theory, based on the ordinary quasi-transverse electromagnetic approach, makes use of multiconductor modal analysis tools where azymuthally coupled even and odd modes play a key role. Results concerning ring voltages and currents, ring input impedance, and ring resonance frequencies are developed. Novel results are compared with those obtained by using the standard approach valid for narrow strip. Radiation effects have been neglected.
A New Efficient Threshold Ring Signature Scheme Based on Coding Theory

Ring signatures were introduced by Rivest, Shamir, and Tauman in 2001. These signatures allow a signer to anonymously authenticate a message on behalf of a group of his choice. This concept was then extended by Bresson, Stern, and Szydlo into t-out-of-N (threshold) ring signatures in 2002. We propose in this article a generalization of Stern's code-based identification (and signature) scheme to design a practical t -out-of- N threshold ring signature scheme. The size of the resulting signatures is in O(N) and does not depend on t , contrary to most of the existing protocols. Our scheme is existentially unforgeable under a chosen message attack in the random oracle model assuming the hardness of the minimum distance problem, is unconditionally source hiding, has a very short public key and has an overall complexity in O(N). This protocol is the first efficient code-based ring signature scheme and the first code-based threshold ring signature scheme. Moreover it has a better complexity than number-theory based schemes which have a complexity in O(Nt). This paper is an extended version of a paper published in the conference PQCrypto 2008, with complete proofs and definitions.
Learning to Optimize via Information-Directed Sampling

We propose information-directed sampling - a new algorithm for online optimization problems in which a decision-maker must balance between exploration and exploitation while learning from partial feedback. Each action is sampled in a manner that minimizes the ratio between the square of expected single-period regret and a measure of information gain: the mutual information between the optimal action and the next observation. We establish an expected regret bound for information-directed sampling that applies across a very general class of models and scales with the entropy of the optimal action distribution. For the widely studied Bernoulli and linear bandit models, we demonstrate simulation performance surpassing popular approaches, including upper confidence bound algorithms, Thompson sampling, and knowledge gradient. Further, we present simple analytic examples illustrating that information-directed sampling can dramatically outperform upper confidence bound algorithms and Thompson sampling due to the way it measures information gain.
The Golgi apparatus in the endomembrane-rich gastric parietal cells exist as functional stable mini-stacks dispersed throughout the cytoplasm

Background information. Acid‐secreting gastric parietal cells are polarized epithelial cells that harbour highly abundant and specialized, H+, K+ ATPase‐containing, tubulovesicular membranes in the apical cytoplasm. The Golgi apparatus has been implicated in the biogenesis of the tubulovesicular membranes; however, an unanswered question is how a typical Golgi organization could regulate normal membrane transport within the membrane‐dense cytoplasm of parietal cells.
Trader Anonymity, Price Formation and Liquidity

Using data from the Frankfurt Stock Exchange we analyze price formation and liquidity in a non-anonymous environment with similarities to the floor of the NYSE. Our main hypothesis is that the non-anonymity allows the specialist to assess the probability that a trader trades on the basis of private information. He uses this knowledge to price discriminate. This can be achieved by quoting a large spread and granting price improvement to traders deemed uninformed. Consistent with our hypothesis we find that price improvement reflects lower adverse selection costs but does not lead to a reduction in the specialist's profit. Further, the quote adjustment following transactions at the quoted bid or ask price is more pronounced than the quote adjustment after transactions at prices inside the spread. Our results indicate that anonymity comes at the cost of higher adverse selection risk.
Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA

Programmed translational frameshifts efficiently alter a translational reading frame by shifting the reading frame during translation. A +1 frameshift has two simultaneous requirements: a translational pause which occurs when either an inefficiently recognized sense or termination codon occupies the A site, and the presence of a special peptidyl-tRNA occupying the P site during the pause. The special nature of the peptidyl-tRNA reflects its ability to slip +1 on the mRNA or to facilitate binding of an incoming aminoacyl-tRNA out of frame in the A site. This second mechanism suggested that in some cases the first +1 frame tRNA could have an active role in frameshifting. We found that overproducing this tRNA can drive frameshifting, surprisingly regardless of whether frameshifting occurs by peptidyl-tRNA slippage or out-of-frame binding of aminoacyl-tRNA. This finding suggests that in both cases, the shift in reading frame occurs coincident with formation of a cognate codon-anticodon interaction in the shifted frame.
Occupational exposure to organic dust increases lung cancer risk in the general population

Background Organic dust is a complex mixture of particulate matter from microbial, plant or animal origin. Occupations with exposure to animal products have been associated with an increased lung cancer risk, while exposure to microbial components (eg, endotoxin) has been associated with a decreased risk. To date there has not been a comprehensive evaluation of the possible association between occupational organic dust exposure (and its specific constituents) and lung cancer risk in the general population. Methods The SYNERGY project has pooled information on lifetime working and smoking from 13 300 lung cancer cases and 16 273 controls from 11 case–control studies conducted in Europe and Canada. A newly developed general population job-exposure matrix (assigning no, low or high exposure to organic dust, endotoxin, and contact with animals or fresh animal products) was applied to determine level of exposure. ORs for lung cancer were estimated by logistic regression, adjusted for age, sex, study, cigarette pack-years, time since quitting smoking, and ever employment in occupations with established lung cancer risk. Results Occupational organic dust exposure was associated with increased lung cancer risk. The second to the fourth quartile of cumulative exposure showed significant risk estimates ranging from 1.12 to 1.24 in a dose-dependent manner (p<0.001). This association remained in the highest quartile after restricting analyses to subjects without chronic obstructive pulmonary disease or asthma. No association was observed between lung cancer and exposure to endotoxin or contact with animals or animal products. Conclusion Occupational exposure to organic dust was associated with increased lung cancer risk in this large pooled case–control study.
Use of Marble Dust in Road Construction

ABSTRACT An attempt has been made to evaluate the effectiveness of using marble dust as filler in bituminous concrete. To compare the results, two other types of filler namely lime and stone dust were also used and various tests like Marshall stability test, unconfined compression test, indirect tensile test and fatigue test were conducted. It was observed that maximum Marshall stability of 15.4 KN was at 7.6% lime filler. Higher compressive strength, modulus of elasticity and tensile strength was obtained with marble dust filler. The maximum compressive strength at 5% marble dust filler was 7.34 N/mm2. The modulus of elasticity and the maximum tensile strength of the mix at 7.0% marble dust filler were 85.18 N/mm2.and 1.82 N/mm2, respectively. The behaviour of bituminous concrete with marble dust filler showed better strength value.
Fraternal Resemblance in Educational Attainment and Occupational Status

This article develops simple structural equation models of the regression of occupational status on schooling in a sample of 518 Wisconsin high school graduates and their brothers. The models correct for response variability and incorporate a family variance component structure. Methodological complications follow from the facts that the sample consists of sibling pairs; that members of a cohort of high school graduates, rather than their families, are the sampling units; and that the primary respondents are informants about some of the characteristics of their brothers. The regression of occupational status on educational attainment is relatively insensitive both to response variability and to the specification of common family factors. Family membership accounts for about half the variance in schooling and more than one-third of the variance in occupational standing, but there is little evidence that failure to control family background leads to upward bias in estimates of the effect of schooling on occupational status.
Evaluation of a Smartphone App for Forest Sample Plot Measurements

We evaluated a smartphone app (TRESTIMATM) for forest sample plot measurements. The app interprets imagery collected from the sample plots using the camera in the smartphone and then estimates forest inventory attributes, including species-specific basal areas (G) as well as the diameter (DgM) and height (HgM) of basal area median trees. The estimates from the smartphone app were compared to forest inventory attributes derived from tree-wise measurements using calipers and a Vertex height measurement device. The data consist of 2169 measured trees from 25 sample plots (32 m × 32 m), dominated by Scots pine and Norway spruce from southern Finland. The root-mean-square errors (RMSEs) in the basal area varied from 19.7% to 29.3% and the biases from 11.4% to 18.4% depending on the number of images per sample plot and image shooting location. DgM measurement bias varied from −1.4% to 3.1% and RMSE from 5.2% to 11.6% depending on the tree species. Respectively, HgM bias varied from 5.0% to 8.3% and RMSE 10.0% to 13.6%. In general, four images captured toward the center of the plot provided more accurate results than four images captured away from the plot center. Increasing the number of captured images per plot to the analyses yielded only marginal improvement to the results.
Plasma Thyroid Hormone Concentrations in a Wintering Passerine Bird: Their Relationship to Geographic Variation, Environmental Factors, Metabolic Rate, and Body Fat

Winter acclimatization among passerine birds involves metabolic adjustments that allow for high rates of thermogenesis. In previous studies, we observed geographic variation in the basal metabolic rate (BMR) of overwintering cardinals along a latitudinal gradient at two different longitudinal transects. Because thyroid hormones (THs) are important for metabolic adjustments in endotherms, we determined whether geographic variation in BMR can be explained by variation in thyroid status. We measured total plasma TH (thyroxine [T4] and 3,5,3′‐triiodothyronine [T3]) concentrations by radioimmunoassay in birds from two latitudinal transects extending from approximately 31° to 42°. Birds from both transects had higher plasma THs in the late afternoon than in the early morning. Plasma T3 increased with latitude, while plasma T4 varied such that the southernmost birds and the northernmost birds had higher hormone concentrations than birds at the intermediate latitude. There was no correlation between plasma TH concentrations and BMR. To test whether thyroid status influences metabolic parameters in winter‐acclimatized captive cardinals, we fed cardinals diets supplemented with T4 (5 μg T4 g−1 food), the goitrogen methimazole (1 mg g−1 food), or both. Plasma T4 concentrations were altered by most of the treatments, but we observed no significant effects on any metabolic parameter. We conclude, therefore, that there is latitudinal variation in metabolic parameters in cardinals but that this variation is not explained by variation in plasma TH concentrations.