Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the Functional Limitations of Lipids and Fatty Acids for Diet Determination: The Importance of Tissue Type, Quantity, and Quality

Lipid and fatty acid (FA) analysis is commonly used to describe the trophic ecology of an increasing number of taxa. However, the applicability of these analyses is contingent upon the collection and storage of sufficient high quality tissue, the limitations of which are previously unexplored in elasmobranchs. Using samples from 110 white sharks, Carcharodon carcharias, collected throughout Australia, we investigated the importance of tissue type, sample quantity, and quality for reliable lipid class and FA analysis. We determined that muscle and sub-dermal tissue contain distinct lipid class and FA profiles, and were not directly comparable. Muscle samples as small as 12 mg dry weight (49 mg wet weight), provided reliable and consistent FA profiles, while sub-dermal tissue samples of 40 mg dry weight (186 mg wet weight) or greater were required to yield consistent profiles. This validates the suitability of minimally invasive sampling methods such as punch biopsies. The integrity of FA profiles in muscle was compromised after 24 hours at ambient temperature (~20°C), making these degraded samples unreliable for accurate determination of dietary sources, yet sub-dermal tissue retained stable FA profiles under the same conditions, suggesting it may be a more robust tissue for trophic ecology work with potentially degraded samples. However, muscle samples archived for up to 16 years in -20°C retain their FA profiles, highlighting that tissue from museum or private collections can yield valid insights into the trophic ecology of marine elasmobranchs.
Power generation in isolated and regional communities: Application of a doubly-fed induction generator based wind turbine

The application of a Doubly Fed Induction Generator (DFIG) as a suitable generating scheme in a remote or isolated communities is presented in this paper. Remote Area Power Supply (RAPS) system, a dummy load and its controller with Energy Storage System (ESS) are identified as the key components. The dummy load is used to absorb the power associated with over generation. The battery storage system is used as a storage buffer which could absorb or release the power into the RAPS system when required. It is also used as a secondary control for the DC link voltage of the back-back converter of the DFIG. The hybrid operation of the DFIG, dummy load, ESS and main load is discussed in relation to the system voltage,frequency and DC link stability. The entire hybrid model has been developed using the SimPowerSystem tool box in MATLAB.
The Role of Community and Social Metrics in Ontology Evaluation: An Interview Study of Ontology Reuse

Finding a "good" or the "right" ontology for reuse is an ongoing challenge in the field of ontology engineering, where the main aim is to share and reuse existing semantics. This paper reports on a qualitative study with interviews of ontologists and knowledge engineers in different domains, ranging from biomedical field to manufacturing industry, and investigates the challenges they face while searching, evaluating, and selecting an ontology for reuse. Analysis of the interviews reveals diverse sets of quality metrics that are used when evaluating the quality of an ontology. While some of the metrics have already been mentioned in the literature, the findings from our study identify new sets of quality metrics such as community and social related metrics. We believe that this work represents a noteworthy contribution to the field of ontology engineering, with the hope that the research community can further draw on these initial findings in developing relevant quality metrics and ontology search and selection.
Private Set Intersection for Unequal Set Sizes with Mobile Applications

Abstract Private set intersection (PSI) is a cryptographic technique that is applicable to many privacy-sensitive scenarios. For decades, researchers have been focusing on improving its efficiency in both communication and computation. However, most of the existing solutions are inefficient for an unequal number of inputs, which is common in conventional client-server settings. In this paper, we analyze and optimize the efficiency of existing PSI protocols to support precomputation so that they can efficiently deal with such input sets. We transform four existing PSI protocols into the precomputation form such that in the setup phase the communication is linear only in the size of the larger input set, while in the online phase the communication is linear in the size of the smaller input set. We implement all four protocols and run experiments between two PCs and between a PC and a smartphone and give a systematic comparison of their performance. Our experiments show that a protocol based on securely evaluating a garbled AES circuit achieves the fastest setup time by several orders of magnitudes, and the fastest online time in the PC setting where AES-NI acceleration is available. In the mobile setting, the fastest online time is achieved by a protocol based on the Diffie-Hellman assumption.
MiR-21 upregulation induced by promoter zone histone acetylation is associated with chemoresistance to gemcitabine and enhanced malignancy of pancreatic cancer cells.

BACKGROUND AND AIMS MicroRNA-21 (miR-21) is reported to be overexpressed and to contribute to proliferation, apoptosis and gemcitabine resistance in pancreatic ductal adenocarcinomas (PDACs). The aims of this study were to explore regulation of miR-21 expression by epigenetic change and its impact on chemoresistance and malignant properties of of pancreatic cancer. MATERIALS AND METHODS We retrospectively collected 41 cases of advanced pancreatic cancer patients who were sensitive or resistant to gemcitabine and assessed levels of serum circulating miR-21 for correlation with cytotoxic activity. Histone acetylation in the miR-21 promoter was also studied in gemcitabine-sensitive and gemcitabine-resistant PDAC cells. Gemcitabine-resistant HPAC and PANC-1 cells were transfected with pre-miR-21 precursors (pre-miR-21) and antisense oligonucleotides (anti-miR-21), and were treated with TSA. Finally, invasion and metastasis assays were performed and alteration in mir-21, PTEN, AKT and pAKT level was evaluated in these cells. RESULTS Serum miR-21 levels were increased in gemcitabine- resistant PDAC patients compared with gemcitabine-sensitive subjects. The miR-21 levels were increased in 6 PDAC cells treated with gemcitabine significantly, associated with 50% inhibitory concentrations (IC50s). Histone acetylation levels at miR-21 promoter were increased in PDAC cells after treatment with gemcitabine. Enhanced invasion and metastasis, increased miR-21 expression, decreased PTEN, elevated pAKT level were demonstrated in gemcitabine-resistant HPAC and PANC-1 cells. Pre-miR-21 transfection or TSA treatment further increased invasion and metastasis ability, decreased PTEN, and elevated pAKT levels in these two lines. In contrast, anti-miR-21 transfection could reverse invasion and metastasis, and PTEN and pAKT expressions induced by gemcitabine. CONCLUSIONS MiR-21 upregulation induced by histone acetylation in the promoter zone is associated with chemoresistance to gemcitabine and enhanced malignant potential in pancreatic cancer cells.
Intensive Combination Chemotherapy and X-Irradiation in Hodgkin's Disease.

Summary A pilot study was begun in 1963 to test the feasibility of using in the treatment of Hodgkin9s disease a combination of cyclophosphamide, vincristine, methotrexate, and prednisone in full doses followed by radiotherapy where indicated. It was found that this form of therapy could be used without a prohibitive cost in toxicity. It appears that the incidence of complete remissions can be increased over that obtained with a single agent. Radiotherapy was tolerated after intensive chemotherapy, and further intensive chemotherapy was possible following high dose but limited field radiation. As expected, toxicity was increased when both modalities of therapy were employed. The duration of complete unmaintained remission in those patients with advanced disease is provocative even though the group is small. It is our feeling that these results invite further investigation of the use of effective agents in combination.
CTLA-4 upregulation during HIV infection: association with anergy and possible target for therapeutic intervention

Objective To study the role of cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) during HIV infection. Methods Intracellular CTLA-4 expression, determined by flow-cytometry, and proliferative responses to HIV antigens, were studied in peripheral blood mononuclear cells (PBMC) from 93 HIV-1-infected [HIV(+)] patients and 40 HIV-1 seronegative controls. Results The proportions of CTLA-4 expressing CD4+ T cells were: (1) significantly higher in HIV(+) patients, 10.95 ± 0.66%, than in controls, 6 ± 0.45% (P < 0.0001); (2) inversely correlated to CD4+ counts (r = −0.67, P < 0.005, n = 16, drug-naive patients;r = −0.57, P < 0.0001, n = 77, HAART-treated patients); and (3) positively correlated to proportion of activated (HLA-DR+CD3+) (r = 0.53, P < 0.0001) and memory (CD45RO+CD4+) T cells (r = 0.46, P < 0.001). CD28 median fluorescence intensity in CTLA-4- cells was twice that in CTLA-4+ cells (140 ± 5.3 versus 70 ± 2.28, P < 0.00001), whereas cells low in CD28 and CD4, expressed more CTLA-4 (P < 0.0001). Higher proportion of CTLA-4+CD4+ cells expressed CCR5 and Ki-67, in comparison with CTLA-4-CD4+ cells, (65 ± 11.9 and 25 ± 7.5% versus 27 ± 8.9 and 3.7 ± 2%, P < 0.0001 and P < 0.01, respectively). Among HAART-treated patients, with viral load below detectable levels, CD4+ cells increase was inversely correlated to %CTLA-4+CD4+ cells (r = −0.5, P = 0.003, n = 39). Proliferation of PBMC to anti-CD3, gp-120 depleted HIV-1 antigen or HIV-1 p24 stimulation was inversely correlated with CTLA-4 levels (r = −0.68, P = 0.0035;r = −0.38, P = 0.04; and r = −0.43, P = 0.028, respectively). Conclusions (1) CTLA-4 is upregulated during HIV infection and may therefore account for CD4 T-cell decline and anergy in HIV-1 infection. (2) Increased levels of CTLA-4 may undermine immune responses and in the HAART-treated patient-immune reconstitution. (3) Blocking of CTLA-4 may offer a novel approach for immune-based therapy in HIV infection.
A novel seamless transferring control method for microgrid based on master-slave configuration

In order to alleviate the growing energy contradiction and maximize use of renewable energy, microgrid is experiencing a rapid development as a new means of power system. The master inverter in microgrid should operate in grid-connected mode and island mode. A seamless transferring control method was presented in this paper, two different control loops were designed for respective operation modes, and the detailed design steps and the improved control method for smooth transition were discussed. A novel phase-locked loop control method applied in microgrid is also proposed, which can ensure the seamless transferring process. Finally, a dedicated microgrid test-bed were built to evaluate the seamless transferring control method, the experimental results in various microgrid operation modes were depicted to demonstrate the correctness of theoretical analysis and the feasibility of the microgrid control strategy.
Multiple-rate multiple-length QC-LDPC codes design with near shannon limit performance

Multiple-rate multiple-length LDPC codes with near Shannon limit performance at each rate are demanded in the next generation digital television terrestrial broadcasting (DTTB) systems. Row-Combining with Edge Variation (RCEV) codes, which generate higher rate codes by linearly combining the rows of parity-check matrix of a lower rate mother code, are rate-compatible with constant code length and simple hardware decoder architecture. This paper proposes an improved multi-rate scheme called Row-Combing-Splitting with Edge Variation (RCSEV) codes, where row splitting is introduced to improve the freedom of code construction at each rate. Multi-length code design can also be achieved by RCSEV codes with Quasi-Cycle (QC) structure. Finally, a set of multi-rate, multi-length candidate codes are proposed for the next generation DTTB systems. A comparison with DVB-S2 LDPC codes is performed and the better performance of our proposed code is validated via both extrinsic information transfer (EXIT) chart analysis and bit error rate (BER) simulations. Hardware implementation result demonstrates that the complexity of the multi-rate decoder is close to that of single rate counterpart.
Current Sheet Permeability in Electromagnetic Pulsed Plasma Thrusters

A case is made for the existence of permeability of current sheets in electromagneticpulsed plasma thrusters. Permeability refers to the leakage of plasma or neutral par-ticles behind the sheet and could cause a signiﬁcant eﬀect on the performance of thethruster. Analytical calculations are presented which demonstrate the mismatch be-tween experimental velocity proﬁles and theoretical snowplow performances. Electrondensity measurements show a signiﬁcant plasma wake following the sheet. Argumentsare also presented based on these data, that in some cases the accelerating plasma sheetentrains less than one third of the propellant. An index of permeability is deﬁned asa ratio of sheet-trailing mass to encountered propellant mass. It may be quantiﬁedeither by directly measuring the trailing mass, or by measuring the mass entrained bythe sheet. The diagnostics needed to measure this index are discussed.I. INTRODUCTION
Toxoplasma gondii: history and diagnostic test development

Abstract Toxoplasma gondii is a protozoa that causes toxoplasmosis in people and other animals. It is considered one of the most common parasitic infections in the world due to its impressive range of hosts, widespread environmental contamination and the diverse means by which animals can be infected. Despite its ubiquity and numerous ongoing research efforts into both its basic biology and clinical management, many aspects of diagnosis and management of this disease are poorly understood. The range of diagnostic options that is available for veterinary diagnostic investigators are notably more limited than those available to medical diagnosticians, making accurate interpretation of each test result critical. The current review joins other reviews on the parasite with a particular emphasis on the history and continued development of diagnostic tests that are useful for veterinary diagnostic investigations. An understanding of the strengths and shortcomings of current diagnostic techniques will assist veterinary and public health officials in formulating effective treatment and control strategies in diverse animal populations.
Systematic biochemical analysis of somatic missense mutations in DNA polymerase β found in prostate cancer reveal alteration of enzymatic function

DNA polymerase β is essential for short‐patch base excision repair. We have previously identified 20 somatic pol β mutations in prostate tumors, many of them missense. In the current article we describe the effect of all of these somatic missense pol β mutations (p.K27N, p.E123K, p.E232K, p.P242R, p.E216K, p.M236L, and the triple mutant p.P261L/T292A/I298T) on the biochemical properties of the polymerase in vitro, following bacterial expression and purification of the respective enzymatic variants. We report that all missense somatic pol β mutations significantly affect enzyme function. Two of the pol β variants reduce catalytic efficiency, while the remaining five missense mutations alter the fidelity of DNA synthesis. Thus, we conclude that a significant proportion (9 out of 26; 35%) of prostate cancer patients have functionally important somatic mutations of pol β. Many of these missense mutations are clonal in the tumors, and/or are associated with loss of heterozygosity and microsatellite instability. These results suggest that interfering with normal polymerase β function may be a frequent mechanism of prostate tumor progression. Furthermore, the availability of detailed structural information for pol β allows understanding of the potential mechanistic effects of these mutants on polymerase function. Hum Mutat 32:1–9, 2011. © 2011 Wiley‐Liss, Inc.
Progression of cerebral white matter lesions in Alzheimer’s disease: a new window for therapy?

Background: White matter lesions (WML) are a risk factor for Alzheimer’s disease. Progression of WML is associated with vascular factors and cognitive decline in population based studies but the course of WML is unknown in Alzheimer’s disease. Objective: To investigate the prevalence and risk factors for progression of WML in Alzheimer’s disease. Subjects: 38 patients with Alzheimer’s disease for whom blood pressure measurements and sequential brain MRIs were available. Methods: The proportion of patients with progression of WML was calculated, stratified on baseline absence or presence of WML by analysis of variance. Odds ratios (OR) were calculated by age and sex adjusted logistic regression to quantify the relation between blood pressure and progression of WML. Results: About 25% of the patients showed progression of WML. Patients with WML at baseline had significantly more progression than those without WML at baseline (adjusted mean difference = 1.2; 95% confidence interval (CI), 0.6 to 1.8). Diastolic blood pressure (DBP) was particularly related to progression of WML (OR = 5.9 (95% CI, 1.0 to 37.6) per 10 mm Hg DBP, p = 0.05). Conclusions: Alzheimer’s disease patients with WML at baseline are at risk for rapid progression of WML. WML may offer a potential treatment target in this disease to ameliorate the rate of cognitive decline.
List of fishes collected in 1883 and 1885 by Pierre Louis Jouy and preserved in the United States National Museum, with descriptions of six new species

During the year 1883 the late Pierre Louis Jouy, then an assistant to the U.S. National Museum, visited Japan, making a small but very valuable collection of rare forms of fishes, many of which he obtained from the markets of Yokohama. During 1885, on his way to Korea, he also visited Sasuna, the port of the Japanese island of Tsushima, in the Straits of Korea. In the present paper is given a list of the species collected in 1883 and 1885, with descriptions of new ones, accompanied by plates drawn by Mr. William Sackston Atkinson, Miss Lydia M. Hart, and Mrs. Chloe Leslie Starks. A few Japanese fishes from other sources contained in the U. S. National Museum are also mentioned. Comparisons have been made with specimens in the very large Japanese collections, as yet undescribed, made by the writers in 1900. The specimens mentioned are in the U. 8. National Museum, a few duplicates being retained for the museum of Stanford University. The writers are under obligation to Mr. Richard Rathbun and to Mr. Barton A. Bean for many favors in connection with the study of this collection.
Mining typos in text

Most forms of text contain typos and many algorithms have been proposed to find them, but not much attention has been paid to understanding the occurrence of typos and their indirect significance in understanding how humans interact through text. In this paper we propose some ways in which typos can be exploited to reveal details about human interaction and closeness. We also look at how they can be used to improve automatic document classification into formal and informal types.
Gel-based Protease Proteomics for Identifying the Novel Calpain Substrates in Dopaminergic Neuronal Cell*

Background: It is important to assess contribution of calpain activation and identify substrates affected during neurodegeneration. Results: Gel-based protease proteomics identified novel substrates that were cleaved in neurotoxin-treated culture and rat brain disease models. Conclusion: These novel calpain substrates may confer protection against neurodegeneration. Significance: Our findings contribute to better deciphering the molecular mechanism underlying the progression of protease-mediated neurodegeneration. Calpains are a family of calcium-dependent cysteine proteases that are ubiquitously expressed in mammals and play critical roles in neuronal death by catalyzing substrate proteolysis. Here, we developed two-dimensional gel electrophoresis-based protease proteomics to identify putative calpain substrates. To accomplish this, cellular lysates from neuronal cells were first separated by pI, and the immobilized sample on a gel strip was incubated with a recombinant calpain and separated by molecular weight. Among 25 altered protein spots that were differentially expressed by at least 2-fold, we confirmed that arsenical pump-driving ATPase, optineurin, and peripherin were cleaved by calpain using in vitro and in vivo cleavage assays. Furthermore, we found that all of these substrates were cleaved in MN9D cells treated with either ionomycin or 1-methyl-4-phenylpyridinium, both of which cause a calcium-mediated calpain activation. Their cleavage was blocked by calcium chelator or calpain inhibitors. In addition, calpain-mediated cleavage of these substrates and its inhibition by calpeptin were confirmed in a middle cerebral artery occlusion model of cerebral ischemia, as well as a stereotaxic brain injection model of Parkinson disease. Transient overexpression of each protein was shown to attenuate 1-methyl-4-phenylpyridinium-induced cell death, indicating that these substrates may confer protection of varying magnitudes against dopaminergic injury. Taken together, the data indicate that our protease proteomic method has the potential to be applicable for identifying proteolytic substrates affected by diverse proteases. Moreover, the results described here will help us decipher the molecular mechanisms underlying the progression of neurodegenerative disorders where protease activation is critically involved.