nils-herrmann/clean_scirepeval huggingface dataset:
Thyroglobulin From Molecular and Cellular Biology to Clinical Endocrinology.
Venue: Endocrine reviews

Thyroglobulin (Tg) is a vertebrate secretory protein synthesized in the thyrocyte endoplasmic reticulum (ER) where it acquires N linked glycosylation and conformational maturation (including formation of many disulfide bonds) leading to homodimerization. Its primary functions include iodide storage and thyroid hormonogenesis. Tg consists largely of repeating domains, and many tyrosyl residues in these domains become iodinated to form monoiodo and diiodotyrosine, whereas only a small portion of Tg structure is dedicated to hormone formation. Interestingly, evolutionary ancestors, dependent upon thyroid hormone for development, synthesize thyroid hormones without the complete Tg protein architecture. Nevertheless, in all vertebrates, Tg follows a strict pattern of region I, II III, and the cholinesterase like (ChEL) domain. In vertebrates, Tg first undergoes intracellular transport through the secretory pathway, which requires the assistance of thyrocyte ER chaperones and oxidoreductases, as well as coordination of distinct regions of Tg, to achieve a native conformation. Curiously, regions II III and ChEL behave as fully independent folding units that could function as successful secretory proteins by themselves. However, the large Tg region I (bearing the primary T4 forming site) is incompetent by itself for intracellular transport, requiring the downstream regions II III and ChEL to complete its folding. A combination of nonsense mutations, frameshift mutations, splice site mutations, and missense mutations in Tg occurs spontaneously to cause congenital hypothyroidism and thyroidal ER stress. These Tg mutants are unable to achieve a native conformation within the ER, interfering with the efficiency of Tg maturation and export to the thyroid follicle lumen for iodide storage and hormonogenesis.
Urinary iodine, thyroid function, and thyroglobulin as biomarkers of iodine status.
Venue: The American journal of clinical nutrition

The accurate assessment of population iodine status is necessary to inform public health policies and clinical research on iodine nutrition, particularly the role of iodine adequacy in normal neurodevelopment. Urinary iodine concentration (UIC) directly reflects dietary iodine intake and is the most common indicator used worldwide to assess population iodine status. The CDC established the Ensuring the Quality of Iodine Procedures program in 2001 to provide laboratories that measure urinary iodine with an independent assessment of their analytic performance; this program fosters improvement in the assessment of UIC. Clinical laboratory tests of thyroid function (including serum concentrations of the pituitary hormone thyrotropin and the thyroid hormones thyroxine and triiodothyronine) are sometimes used as indicators of iodine status, although such use is often problematic. Even in severely iodine deficient regions, there is a great deal of intraindividual variation in the ability of the thyroid to adapt. In most settings and in most population subgroups other than newborns, thyroid function tests are not considered sensitive indicators of population iodine status. However, the thyroid derived protein thyroglobulin is increasingly being used for this purpose. Thyroglobulin can be measured in either serum or dried blood spot (DBS) samples. The use of DBS samples is advantageous in resource poor regions. Improved methodologies for ascertaining maternal iodine status are needed to facilitate research on developmental correlates of iodine status. Thyroglobulin may prove to be a useful biomarker for both maternal and neonatal iodine status, but validated assay specific reference ranges are needed for the determination of iodine sufficiency in both pregnant women and neonates, and trimester specific ranges are possibly needed for pregnant women. UIC is currently a well validated population biomarker, but individual biomarkers that could be used for research, patient care, and public health are lacking.
An interaction based approach to detecting highly interactive Twitter communities using tweeting links
Venue: Web Intell.

The immense popularity and rapid growth of Online Social Networks (OSN) have attracted the interest of researchers and companies, particularly in how users group together to form communities online. While many community detection algo rithms have been developed to detect communities on such OSNs, most of these algorithms are based only on topological links and researchers have observed that many topological links do not translate to actual user interaction. As such, many members of the detected communities do not communicate frequently to each other. This inactivity creates a problem in targeted adver tising and viral marketing, which require the community to be highly active so as to facilitate the diffusion of product/service information. We propose an approach to detect highly interactive Twitter communities that share common interests, based on the frequency and patterns of direct tweeting among users, rather than the topological information implicit in follower/following links. Our experimental results show that communities detected by our proposed approach are more cohesive and connected within different interest groups, based on topological measures. We also show that the detected communities actively interact about the specific interests, based on the high frequency of #hashtags and @mentions related to this interest. In addition, we study the trends in their tweeting patterns such as how they follow and unfollow other users, and observe that our approach detects communities comprising users whose links are more persistent compared to those in other groups of users.
Querying and Tracking Influencers in Social Streams
Venue: WSDM

Influence analysis is an important problem in social network analysis due to its impact on viral marketing and targeted advertisements. Most of the existing influence analysis methods determine the influencers in a static network with an influence propagation model based on pre defined edge propagation probabilities. However, none of these models can be queried to find influencers in both context and time sensitive fashion from a streaming social data. In this paper, we propose an approach to maintain real time influence scores of users in a social stream using a topic and time sensitive approach, while the network and topic is constantly evolving over time. We show that our approach is efficient in terms of online maintenance and effective in terms various types of real time context and time sensitive queries. We evaluate our results on both social and collaborative network data sets.
Clear piezochromic behaviors of AIE active organic powders under hydrostatic pressure

A novel diphenylacrylonitrile derivative (Z) 3 (4' (diphenylamino) [1,1' biphenyl] 4 yl) 2 (4 methoxyphenyl) acrylonitrile (b CN TPA) containing a twisted triphenylamine and diphenylacetonitrile was synthesized via Knoevenagel condensation and Suzuki coupling reactions. These molecules exhibited aggregation enhanced emission (AIE) effects. Interestingly, their mechano fluorochromic properties were invisible upon grinding with a pestle. However, when hydrostatic pressure in a diamond anvil cell (DAC) was applied on the crystals of b CN TPA, the distinct piezochromic behaviors of the compound were observed. The fluorescence color changed from light green (530 nm) to red (665 nm) with a significant red shift of 135 nm. The powder X ray diffraction and high pressure Raman studies indicated that the as synthesized and ground samples had the same crystalline structures, while the compressed samples had an evident change in inter molecular interactions. Comparative tests and theoretical analysis further confirmed that the distinct fluorescence behaviors of the desired dye during the different stress conditions were associated with the various inter molecular interactions that existed with adjacent molecules.
Clogging of microfluidic systems.
Venue: Soft matter

The transport of suspensions of microparticles in confined environments is associated with complex phenomena at the interface of fluid mechanics and soft matter. Indeed, the deposition and assembly of particles under flow involve hydrodynamic, steric and colloidal forces, and can lead to the clogging of microchannels. The formation of clogs dramatically alters the performance of both natural and engineered systems, effectively limiting the use of microfluidic technology. While the fouling of porous filters has been studied at the macroscopic level, it is only recently that the formation of clogs has been considered at the pore scale, using microfluidic devices. In this review, we present the clogging mechanisms recently reported for suspension flows of colloidal particles and for biofluids in microfluidic channels, including sieving, bridging and aggregation of particles. We discuss the technological implications of the clogging of microchannels and the schemes that leverage the formation of clogs. We finally consider some of the outstanding challenges involving clogging in human health, which could be tackled with microfluidic methods.
Dynamics of bacterial streamers induced clogging in microfluidic devices.
Venue: Lab on a chip

Using a microfabricated porous media mimic platform, we investigated the clogging dynamics of bacterial biomass that accumulated in the device due to the formation of bacterial streamers. Particularly, we found the existence of a distinct clogging front which advanced via pronounced 'stick slip' of the viscoelastic bacterial biomass over the solid surface of the micro pillar. Thus, the streamer, the solid surface, and the background fluidic media defined a clear three phase front influencing these advancing dynamics. Interestingly, we also found that once the clogging became substantial, contrary to a static homogenous saturation state, the clogged mimic exhibited an instability phenomena marked by localized streamer breakage and failure leading to extended water channels throughout the mimic. These findings have implications for design and fabrication of biomedical devices and membrane type systems such as porous balloon catheters, porous stents and filtration membranes prone to bacteria induced clogging as well as understanding bacterial growth and proliferation in natural porous media such as soil and rocks.
Big Data Meaning in the Architecture of IoT for Smart Cities
Venue: DMBD

Internet of Things (IoT) is the technology that allows making interconnections between devices and internet; its applications have been developed to give answer to society's needs and requirements. In the last years, communities have gotten interested into incorporate this and some other Information Technologies to the cities, to make of those Smart Cities. Currently, applications just reply to particular necessities but general structures of IoT are being developed to improve the Smart City functioning and there is where Big Data (Classification and analysis of information) takes an important place inside the architecture, because this area manages the complexity, quantity and the variety of data for the right working of systems and the acquisition of classified useful data in real time. This paper aims to explain the importance of Big Data as Information Technology (IT) to organize and direct correctly the information in complex systems as the involved in the development of the Smart Cities.
Multiscale patch based contrast measure for small infrared target detection
Venue: Pattern Recognit.

Infrared (IR) small target detection plays an important role in IR guidance systems. In this paper, a biologically inspired method called multiscale patch based contrast measure (MPCM) is proposed for small IR target detection. MPCM can increase the contrast between target and background, which makes it easy to segment small target by simple adaptive thresholding method. Experimental results on three sequences demonstrate that the proposed small target detection method can not only suppress background clutter effectively even if with strong noise interference, but also detect targets accurately with low false alarm rate and high speed. HighlightsA biologically inspired target enhancement method called multiscale patch based contrast measure (MPCM) is presented.Based on MPCM, a small IR target detection algorithm is designed.The proposed small target detection method achieves promising detection performance on three real IR image sequences.
A computational tool for evaluating urban vitality using Kendall Square development proposals as a case study

Kendall Square, home to MIT, a world class university and a district known globally for its reputation as an epicenter of ideas and innovation, has recently seen a new wave of development seeking to turn it into a place for people. Typically, multiple developers and private investors will bid on developing the area. The competitive nature of this process suggests that involved parties have varying and potentially conflicting objectives. For example, the soaring office and residential rents in Kendall Square make it attractive to private developers looking for monetary gains. Furthermore, in an area with an already high employment density, the addition of more office and commercial spaces could increase the stress on the public transportation system that is struggling to keep up with current demand. This becomes a design problem with no optimal solution. The question becomes, how do we design districts to be more livable for people? In this research we propose a computational evaluation decision support platform to facilitate collaborations between stakeholders in their interactions within the contexts of urban planning. Whether planned interventions or new developments, the aim of this research is to give stakeholders the ability to weigh the implications from these interventions on the vitality of districts. Chapter 1 lays the foundation of the theoretical contributions put forth by Jane Jacobs regarding urban vitality. Chapter 2 discusses the four diversity conditions for urban vitality and early attempts to validate these conditions. Chapter 3 presents an overview of the urban elements of both Kendall Square and Harvard Square as a case study. In chapter 4 we apply Jacobs' vitality conditions to both case studies. We find that Harvard Square is balanced in terms of Jacobs' conditions, while Kendall Square suffered form an imbalance in residential density. Chapter 5 presents the computational evaluation platform "CityMatrix" and uses the Volpe and MIT development sites as examples of urban interventions. We find that the current plan, approximately 16,000 employees and 3,500 residents is not enough to increase the population density to make Kendall Square a more vital district. Lastly, chapter 6 provides a conclusion and future steps for this research.  Principal Research Scientist of Media Arts and Sciences
Morusin Induces TRAIL Sensitization by Regulating EGFR and DR5 in Human Glioblastoma Cells.
Venue: Journal of natural products

Glioblastoma is one of the most malignant primary tumors, and the prognosis for glioblastoma patients remains poor. Tumor necrosis factor related apoptosis inducing ligand (TRAIL) is considered a promising anticancer agent due to its remarkable ability to selectively kill tumor cells. However, since many cancers are resistant to TRAIL, strategies to overcome resistance are required for the successful use of TRAIL in the clinic. In the present study, the potential of morusin as a TRAIL sensitizer in human glioblastoma cells was evaluated. Treatment with TRAIL or morusin alone showed weak cytotoxicity in human glioblastoma cells. However, combination treatment of TRAIL with morusin synergistically decreased cell viability and increased apoptosis compared with single treatment. Morusin induced expression of death receptor 5 (DR5) but not DR4 or decoy receptors (DcR1 and DcR2) Furthermore, morusin significantly decreased anti apoptotic molecules survivin and XIAP. In addition, morusin reduced expression of EGFR and PDFGR as well as phosphorylation of STAT3, possibly mediating down regulation of survivin and XIAP. Together these results suggest that morusin enhances TRAIL sensitivity in human glioblastoma cells through regulating expression of DR5 and EGFR. Therefore, the combination treatment of TRAIL and morusin may be a new therapeutic strategy for malignant glioma patients.
Dynamic MUSIC: accurate device free indoor localization
Venue: UbiComp

Device free passive indoor localization is playing a critical role in many applications such as elderly care, intrusion detection, smart home, etc. However, existing device free localization systems either suffer from labor intensive offline training or require dedicated special purpose devices. To address the challenges, we present our system named MaTrack, which is implemented on commodity off the shelf Intel 5300 Wi Fi cards. MaTrack proposes a novel Dynamic MUSIC method to detect the subtle reflection signals from human body and further differentiate them from those reflected signals from static objects (furniture, walls, etc. to identify the human target's angle for localization. MaTrack does not require any offline training compared to existing signature based systems and is insensitive to changes in environment. With just two receivers, MaTrack is able to achieve a median localization accuracy below 0.6 m when the human is walking, outperforming the state of the art schemes.
The political economy of pricing and capacity decisions for congestible local public goods in a federal state

This paper studies the political economy of pricing and investment for excludable and congestible public goods in a federal state. Although the model applies to many local congestible public facilities (such as libraries, museums and public swimming facilities) our main motivation is the problem of providing and pricing road infrastructure in federal states. The two region model we develop allows for spill overs between regions, it takes into account congestion, and it captures demand heterogeneity both between and within regions. Regional decisions are taken by majority voting; federal decisions are taken by a minimum winning coalition in a legislature of regionally elected representatives. We have the following results. First, when users form the majority in at least one region, decentralized decision making performs certainly better than centralized decision making if spill overs are not too large. Centralized decisions may yield higher welfare than decentralization only if users have a large majority and the infrastructure in a given region is intensively used by both local and outside users. Second, if non users form a majority in both regions, centralized decision making and decentralized decision making yield the same socially undesirable outcome, with prices that are much too high. Third, the performance of decentralized supply is strongly enhanced by local self financing rules; this prevents potential exploitation of users within regions.
Fast Expanding Markets: The Revolution of the Microeconomy

Where will we find growth opportunities the kind that will take our businesses to the next level? The usual and popular choice of terms we use when looking at current markets and potential ones often include developed markets and emerging economies. These terms have inspired a new golden age of racing to the new treasure hidden in the capacities of these markets. Based on the seminal concept of "fast expanding markets," this article discovers growth as residing at a new level, capable of redefining geographies and territories, often untapped or unnoticed by the most conventional macroeconomic analysis.
Alternative feed ingredients in fish diets: Distiller's dried grains with solubles

Kurutulmus damitma kalintilari ve cozunur maddelerinin (DDGS) basta misir olmak uzere bugday, arpa ve sorgum gibi tahillarda veya karisimlarinda bulunan sekerin enzim ve mayalarla fermantasyonundan sonra karbondioksitin ve etanolun ayrilmasi sonucu geriye kalan kismin kurutulmasi ile elde edilen bir yem hammaddesidir. Yuksek enerji ve orta duzey protein icerigi, nispeten dusuk fosfor orani ve ucuz maliyeti nedeni ile su urunleri yem sektorunde kullanilabilecek onemli bir alternatif yem hammadde kaynagidir. DDGS, bircok bitkisel protein kaynaginda olan anti besinsel madde icermemesi nedeniyle de dikkat cekmektedir. Misirdan elde edilen DDGS genel olarak, %22 37 arasinda ham protein, %3 15 arasinda ham yag, %2 5 ham kul, %5 11 ham seluloz ve dusuk oranda nisasta %4 9) icerigine sahiptir. Yuksek miktarda doymamis yag asidi %86,7) linoleik asit %59, linolenik asit %7,8, DHA %0,14 ve dusuk miktarda doymus yag asidi %13,6) icermektedir. Ayrica %3,9 oraninda maya, %7,6 oraninda b glukan icermesi nedeniyle baliklarin bagisiklik sistemine olumlu katki sagladigi ve patojen organizmalara karsi direnci artirdigi bildirilmektedir.
PNUMATICALLY OPERATED AUTOMATIC PIPE CUTTING MACHINE

Cutting machine is one of the principal machines in industry. Engineers are always developing sophisticated machines and modern techniques have to be continuously developed and executed for economical manufacturing of products. At the same time, we should take precaution that there has been no negotiation made with quality and accuracy. In the age of automation machine grow into an integral part of human being. By the use of mechanization machine demonstrate itself that it gives high production rate than manual manufacture rate. In competitive race market everybody wants to rise their production make their machine flexible. The engineer is regularly conformed to the encounters of bringing ideas and design into reality. New machines and methods are being advanced continuously to manufacture various products at cheaper rates and high quality. So we are going to make a machine for Automatic Pneumatic Pipe Cutting Machine and make it multipurpose should be used as cutting machine is simple to maintain easy to operate. Hence we tried our ideas and concepts on this research project to cut PVC pipes.
Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer
Venue: Scientific reports

Invasive lobular carcinoma (ILC) is the second most frequently occurring histological breast cancer subtype after invasive ductal carcinoma (IDC) accounting for around 10% of all breast cancers. The molecular processes that drive the development of ILC are still largely unknown. We have performed a comprehensive genomic, transcriptomic and proteomic analysis of a large ILC patient cohort and present here an integrated molecular portrait of ILC. Mutations in CDH1 and in the PI3K pathway are the most frequent molecular alterations in ILC. We identified two main subtypes of ILCs: (i) an immune related subtype with mRNA up regulation of PD L1, PD 1 and CTLA 4 and greater sensitivity to DNA damaging agents in representative cell line models; (ii) a hormone related subtype, associated with Epithelial to Mesenchymal Transition (EMT) and gain of chromosomes 1q and 8q and loss of chromosome 11q. Using the somatic mutation rate and eIF4B protein level, we identified three groups with different clinical outcomes, including a group with extremely good prognosis. We provide a comprehensive overview of the molecular alterations driving ILC and have explored links with therapy response. This molecular characterization may help to tailor treatment of ILC through the application of specific targeted, chemo and/or immune therapies.