Miracle-dz/UniFAR-FTUs huggingface dataset:
Visceral organ mass and cellularity in growth-restricted and refed beef steers.

Beef steers were fed in two phases to compare the effects of diet and intake on growth and cellularity of visceral organs. During the growing phase (237 to 327 kg), steers were fed either a high (C) or low (F) concentrate diet. Diet F was available ad libitum (FA), whereas diet C was available either ad libitum (CA) or on a limited basis (CL) to match live weight gains of the FA group. During the finishing phase (327 to 481 kg), all steers received diet C either ad libitum (CA-CA, CL-CA, and FA-CA) or restricted (CL-CL and FA-CL) to 70% of the intakes of corresponding CA steers. Marked nutritional effects on liver growth (e.g., -25 and -15% in CL and FA, respectively, relative to CA) were due mainly to changes in cell size (i.e., protein:DNA), with smaller changes in cell numbers (i.e., DNA). Hyperplasia and hypertrophy played a role in growth of the forestomachs, although cell numbers and sizes tended to change in opposite directions, limiting magnitudes of changes in organ mass. Protein synthetic capacity (i.e., RNA) varied as well, often in parallel with cell number. This result differed from that observed in intestines, which maintained constant cell sizes but underwent marked changes in cell number. For liver, amounts of absorbed nutrients seemed to be the main factor driving hypertrophy. The organs of the gastrointestinal tract responded to physical and chemical signals, as shown by the effects of dietary fiber on growth of the forestomachs and intestines. Forestomachs responded mainly to diet fiber content, whereas the intestines responded to diet type and nutrient supply. Feeding programs for beef animals often include changes in diet type and periods of feed limitation, and these in turn affect visceral organ growth and metabolism. Because visceral organs are a major contributor to whole-body energy expenditures, factors affecting these tissues must be understood. This study supports the concept that workload determines organ size, but dietary factors influencing workload clearly vary for each organ.
The dimerization domain of potato spindle tuber viroid, a possible hallmark for infectious RNA.

Covalently closed circular (+) RNA of the potato spindle tuber viroid (PSTVd) can efficiently dimerize noncovalently upon heating and slow cooling in the presence of monovalent cations or Mg2+. In vitro transcription of subgenomic fragments reveals that the ability to dimerize resides in the "upper strand" of its self-complementary rod-like structure. Nuclease probing of these fragments, namely, molecules spanning either the upper or the lower strand of PSTVd, confirms the existence of the previously proposed hairpins I-III, of which hairpin I might contain noncanonical G.A and A.A base pairs. In addition, the upper and lower (+) strands contain large hairpin loops consisting of stretches rich in either adenosine or uridine. Dimerization of the upper (+) strand results in a nuclease-resistant core encompassing hairpin I and is inhibited by an antisense oligonucleotide spanning the entire hairpin; this palindromic domain thus represents the dimerization site. When upper and lower strands were heated and cooled together, no annealing to a viroid-like duplex of both molecules occurs, only dimerization of the upper strand. Therefore, the dimerization hairpin of viroid RNA represents a unique conformational signal that is homologous to similar regions in the human immunodeficiency virus and other retroviruses.
Hageman factor, platelets and polyphosphates: early history and recent connection

Summary. Platelet activation and blood coagulation are essential for hemostasis and contribute to a variety of other biological processes such as inflammation, complement activation and tissue repair. Factor (F)XII, originally called Hageman factor, plays an important role in the kallikrein‐kinin system by activating prekallikrein. In the 1960s, a platelet activity that promoted FXII activation was identified but its biochemical nature remained unknown. Inorganic polyphosphates (poly P) are polymers that consist of many phosphate residues linked by phosphoanhydride bonds. These polymers exist in all living organisms. In bacteria, poly P is important for growth and survival. Recently, poly P has been identified in human platelet dense granules. Studied have shown that upon platelet activation and secretion, poly P activates FXII, indicating that it is most likely the elusive platelet FXII activator. Poly P also regulates coagulation and fibrinolysis. In this review, we focus on early studies of FXII and the identification of platelet FXII activation activity, and discuss recent findings of poly P in FXII activation and coagulation.
A Novel Neural Network Computing Based Way to Sensor and Method Fusion in Harsh Operational Environments

We address a novel neural network computing-based approach to the problem of near real-time feature enhanced fusion of remote sensing (RS) imagery acquired in harsh sensing environments. The novel proposition consists in adapting the Hopfield-type maximum entropy neural network (MENN) computational framework to solving the RS image fusion inverse problem. The feature enhanced fusion is performed via aggregating the descriptive experiment design with the variational analysis (VA) inspired regularization frameworks that lead to an adaptive procedure for proper adjustments of the MENN synaptic weights and bias inputs. We feature on the considerably speeded-up implementation of the MENN-based RS image fusion and verify the overall image enhancement efficiency via computer simulations with real-world RS imagery.
A skeleton in the atherosclerosis closet.

Routine chest x-rays often reveal calcium mineral deposits of the aorta and cardiac valves, sometimes with a density comparable to that of bone. Since atherosclerosis in the early 1900s was long dismissed as a passive, degenerative, inevitable process of aging, interest in its mechanism has been limited. Calcification in the coronary arteries has been widely regarded as uncommon. Recently, two new imaging methods, ultrafast computed tomography (UFCT) and intravascular ultrasound (IVUS), have changed this impression by revealing mineral deposits in the vast majority of significant lesions and in 90% of patients with coronary artery disease.1 2 UFCT and IVUS studies showed the unexpected result that coronary calcification occurs in the absence of coronary narrowing. In the simplest terms, where there is coronary calcification, there is usually atherosclerosis, but not necessarily stenosis. Some take this to mean that calcification is not a useful marker because it does not diagnose coronary narrowing specifically. Another interpretation is that calcification is a useful marker of early coronary atherosclerosis, in that it occurs long before end-stage disease, during the stage of compensatory enlargement. If this is so—and it agrees with reports of calcification in very young patients with familial hypercholesterolemia3 —coronary calcification may turn out to be useful as a marker for early, not necessarily stenotic, atherosclerosis. Contributing to the notion that calcification is uncommon is the absence of calcified lesions among textbook examples of vascular disease. One reason may be that early calcium deposits are washed out by routine histological preparation.4 In addition, selection bias may occur at several levels: harvesting calcified specimens dulls scalpel blades, sectioning calcified specimens without decalcification damages microtome blades, and fragmentation and strewing of the mineral across sections results in messy photomicrographs unsuitable for publication. In this issue of Circulation , O’Brien and colleagues5 provide …
Silicon Integrated Photonics for Microelectronics Evolution

The advances in Si technology and the rapid growth of broadband communication via optical fiber allow silicon integrated photonics to begin revolutionizing the electronic devices, circuits, and systems. The pace of technological development has been recently speeded up. Using micro fabrication technology we are now able to make waveguide structures and optical components of Si-based materials, such as silicon oxynitride or doped silica. Visible light can be obtained from Si-based materials such as Si quantum wire/dots and Si nanoclusters embedded in insulators. It is further demonstrated that lasing effect is also possible with the nanostructures. The impact of these moves will be revolutionary. Si integrated photonics will enable on-chip optical interconnects for future microprocessor and giga-scale circuits, chip-to-chip fiber interconnection and will greatly decrease the cost for fiber-to-home connection. This will be one of the major moves for the next technology revolution. The present article discusses some recent developments on these aspects
Systemic Levels of Lipid Peroxidation and Its Metabolic and Dietary Correlates in Patients with Nonalcoholic Steatohepatitis

BACKGROUND AND AIM:Products of systemic lipid peroxidation are important in the pathogenesis of cardiovascular disease. Subjects with NASH have increased hepatic lipid peroxidation, but it is unknown if they have increased oxidative stress and lipid peroxidation systemically. Therefore, we conducted a study to measure the circulating levels of lipid peroxidation products and their metabolic and nutritional correlates in patients with NASH and controls.METHODS:Systemic lipid peroxidation was assessed by measuring the levels of oxidized LDL (ox-LDL) and thiobarbituric acid-reacting substances (TBARS) in 21 subjects with NASH and 19 controls. Correlations were made between serum lipid peroxidation and nutritional determinants of oxidative stress and defense, serum lipids, insulin resistance, transaminases, and liver histology. The short-term nutrient intake was analyzed by maintaining a 3-wk dietary diary.RESULTS:The serum levels of ox-LDL were significantly higher in NASH patients compared to controls (56 ± 16 U/L vs 40 ± 12 U/L, respectively, p < 0.001). Similarly, serum TBARS were significantly higher in NASH patients compared to controls (3.4 ± 1.3 vs 1.8 ± 0.9 nmols/ml, respectively, p= 0.0001). Insulin resistance was independently associated with ox-LDL (p= 0.01) and TBARS levels (p= 0.01). We found no differences in the intake of various macro- and micronutrients between the two groups and there was no association between nutrient intake and ox-LDL or TBARS.CONCLUSION:Subjects with NASH have significantly higher systemic levels of lipid peroxidation products and this could indicate an increased risk of cardiovascular disease. More studies are needed to evaluate this possibility.
The Enigmatic Epidemiology of Nasopharyngeal Carcinoma

Nasopharyngeal carcinoma (NPC) has a unique and complex etiology that is not completely understood. Although NPC is rare in most populations, it is a leading form of cancer in a few well-defined populations, including natives of southern China, Southeast Asia, the Arctic, and the Middle East/North Africa. The distinctive racial/ethnic and geographic distribution of NPC worldwide suggests that both environmental factors and genetic traits contribute to its development. This review aims to summarize the current knowledge regarding the epidemiology of NPC and to propose new avenues of research that could help illuminate the causes and ultimately the prevention of this remarkable disease. Well-established risk factors for NPC include elevated antibody titers against the Epstein-Barr virus, consumption of salt-preserved fish, a family history of NPC, and certain human leukocyte antigen class I genotypes. Consumption of other preserved foods, tobacco smoking, and a history of chronic respiratory tract conditions may be associated with elevated NPC risk, whereas consumption of fresh fruits and vegetables and other human leukocyte antigen genotypes may be associated with decreased risk. Evidence for a causal role of various inhalants, herbal medicines, and occupational exposures is inconsistent. Other than dietary modification, no concrete preventive measures for NPC exist. Given the unresolved gaps in understanding of NPC, there is a clear need for large-scale, population-based molecular epidemiologic studies to elucidate how environmental, viral, and genetic factors interact in both the development and the prevention of this disease. (Cancer Epidemiol Biomarkers Prev 2006;15(10):1765–77)
Phytodentistry: use of medicinal plants

Abstract Finding healing powers in plants is an ancient idea. Herbs have been used as a traditional form of medicine since time immemorial. The natural products derived from medicinal plants have proven to be an abundant source of biologically active compounds, many of which have been the basis for the development of new chemicals for pharmaceuticals. Phytodentistry implies the use of plants and their products in the process of treating disease directly or indirectly. A crucial role is played by phytotherapy in the treatment of stomatological problems. It started with the use of miswak (chewing stick), and it is still relevant today as herbal toothpaste in many parts of the country. India is the largest producer of medicinal herbs and is appropriately called the botanical garden of the world. The use of this readily available, natural and safe resource as a part of dental practice has great potential for a more “Natural and Green Dental Practice”. Plant products have long been used in dentistry as part of various dental materials right from impression materials to eugenol, which forms an integral part of the dental clinic. The use of herbs in dental practice is not limited to only material sciences. A single herb shows a variety of effects like anti-inflammatory, antibacterial, antifungal activity and many more. Hence the incorporation of these herbs in dental practice will prove to be a valuable adjunct in dental treatment. This review is aimed at exploring the perspectives of this holistic treatment approach in dentistry and its benefits as an adjunctive therapy.
Radar altimetry of water level variability in the Inner Delta of Niger River

This study shows that consistent long term water level time series could be established in heterogeneous medium such as the Delta, using satellite altimetry data. A correction of 89 cm was used to reduce the two satellites at the same altimetry reference system. The seventeen years of water level data is of great value for hydrologic and climate related studies in the Delta in West-Africa, where measurements gauge stations are rare. Our results show that precipitation has a major influence in the flooding process in the Delta. Further analyses are ongoing to better understand the contributions of satellite altimetry data in the study of the hydrology and climate in the Delta.
RecG helicase promotes DNA double‐strand break repair

Double‐strand breaks pose a major threat to the genome and must be repaired accurately if structural and functional integrity are to be preserved. This is usually achieved via homologous recombination, which enables the ends of a broken DNA molecule to engage an intact duplex and prime synthesis of the DNA needed for repair. In Escherichia coli, repair relies on the RecBCD and RecA proteins, the combined ability of which to initiate recombination and form joint‐molecule intermediates is well understood. To shed light on subsequent events, we exploited the I‐SceI homing endonuclease of yeast to make breaks at I‐SceI cleavage sites engineered into the chromosome. We show that survival depends on RecA and RecBCD, and that subsequent events can proceed via either of two pathways, one dependent on the RuvABC Holliday junction resolvase and the other on RecG helicase. Both pathways rely on PriA, presumably to facilitate DNA replication. We discuss the possibility that classical Holliday junctions may not be essential intermediates in repair and consider alternative pathways for RecG‐dependent separation of joint molecules formed by RecA.
Direct visualization of plasmid DNA in bacterial cells

The direct visualization of plasmid DNA inside Escherichia coli cells is demonstrated using phase‐fluorescence microscopy of DAPI (4′,6‐diamidino‐2‐phenylindole)‐stained bacteria. Small as well as large plasmids could be detected, both in minicells and in cells of larger size. For large plasmids, even single molecules appeared to be within the detection limit. The fluorescence generated from monomers of small plasmids was probably below this limit, and for these plasmids the observed signals may represent aggregates. The distribution of the fluorescence foci might reflect specific plasmid positioning during partition and/or replication.
An integrated module portfolio planning approach for complex products and systems

Modularisation can dramatically shorten the lead time and reduce the cost of the product development. Most of the existing modularisation researches focus on the module partition, which is just the initial stage of an integrated modularisation implementation. With the increasing of the module number, the product design engineers could not obtain the modules satisfying the emerging customer requirements (CRs) from the established module portfolio efficiently, especially in a complex product and system (CoPS) development. The CoPS module portfolio must be carefully established, planned and managed, for which a CoPS module portfolio planning (MPP) framework is proposed to assist the design engineers to obtain the optimal module portfolio in CoPS development. First, the MPP problem for CoPS is modelled as a mixed-integer programming from two perspectives: the cost utility of each parametric module and the information content for the function requirements (FRs) mapped from CRs. Second, the cost utility and the information content are calculated based on the part-worth model and the information axiom, respectively. Third, a heuristic genetic algorithm (GA) is employed to solve the programming. Finally, a large tonnage crawler crane (LTCC) MPP problem is performed as an example to elaborate the effectiveness of the proposed framework.
Frequent TSH receptor genetic alterations with variable signaling impairment in a large series of children with nonautoimmune isolated hyperthyrotropinemia.

CONTEXT Heterozygous mutations in the TSH receptor gene (TSHR) are associated with partial TSH resistance, characterized by isolated nonautoimmune hyperthyrotropinemia (NAHT). The prevalence and management of this condition is controversial. OBJECTIVE Our objective was to investigate the prevalence and clinical impact of TSHR alterations in a large series of pediatric patients with NAHT and to dissect their mechanism of action. DESIGN AND SETTING For this prospective multicenter study, clinical data and samples were collected in the clinical units and conveyed to a centralized laboratory for analysis. PATIENTS Subjects included 153 unrelated patients with NAHT aged <18 yr. Exclusion criteria included thyroid dysgenesis or major associated congenital defects. MAIN OUTCOME MEASURES Parameters of thyroid function, TSHR gene analysis, and TSHR functional assays were evaluated. RESULTS The frequency of heterozygous nonpolymorphic TSHR variations was 11.8%. We identified seven previously unknown variations: a frameshift (p.Q33PfsX46), one intronic (g.IVS4+2A→G), and five novel missense (p.P162L, p.Y466C, p.I583T, p.I607T, and p.R609Q) variations. The missense variations variably affected TSHR membrane expression and G(s) and/or G(q/11) signaling. Several variations cosegregated with NAHT in the affected families. Parameters of thyroid function were similar between affected and unaffected family members. CONCLUSIONS Nonpolymorphic alterations in the TSHR gene are commonly associated with isolated NAHT in young patients, thus configuring partial TSH resistance as the most frequent inheritable cause of isolated NAHT. The identification of TSHR defects may thus be helpful for a tailored management of subclinical hypothyroidism. We provide further evidence that besides the well-known defects in G(s) signaling, TSHR genetic alternations found in NAHT may frequently impair the G(q/11) pathway.
High-Grade Endometrial Carcinoma: Serous and Grade 3 Endometrioid Carcinomas Have Different Immunophenotypes and Outcomes

High-grade endometrial carcinomas are a heterogeneous group of tumors and include grade 3 endometrioid (EC-3), serous (SC), and clear cell carcinomas (CCC). There are conflicting data about the prognosis of these subtypes of high-grade endometrial carcinoma; this may be a result of lack of reproducibility in classifying tumor cell type. The purpose of this study was to examine differences in immunophenotype and outcome in a series of high-grade endometrial carcinomas, focusing on the comparison of EC-3 versus SC. We selected 180 endometrial carcinomas of SC, EC, or CCC type. No mixed carcinomas were included in the study. We chose the following immunohistochemical markers, estrogen receptor (ER), insulin-like growth factor 2 mRNA-binding protein 3 (IMP3), p16, p53, progesterone receptor (PR), and phosphatase and tensin homolog (PTEN) as being significantly differentially expressed in endometrial carcinoma subtypes. The tumors were stratified into 4 groups on the basis of their cell type and grade: EC grade 1 or 2, EC-3, SC, and CCC. Univariate survival analysis revealed significant differences in outcome between the 4 groups (P<0.0001), with significantly longer disease-specific survival for grade 1 or 2 EC versus EC-3 (P=0.0001), and EC-3 versus SC (P=0.0003). p16, PTEN, and IMP3 expression was observed more frequently in SC compared with EC-3 (P<0.0001, P=0.021, and P=0.031, respectively). These 3 markers showed the highest sensitivity and specificity in distinguishing between EC-3 and SC, with receiver operating characteristics area under the curve of 0.85, 0.69, and 0.71, respectively. ER and p53 approached but did not reach significance for differential expression in EC-3 versus SC (P=0.055 and P=0.068, respectively). A combination of p16 and PTEN predicts EC-3 versus SC with a sensitivity of 90.0% and specificity of 96.8%. p16 and PTEN can aid in distinguishing between EC-3 and SC of the endometrium, and are superior to ER, PR, and p53 for this purpose. EC-3 carcinomas have a significantly better prognosis than SC carcinomas of the endometrium.
Novel alleles of the chemokine-receptor gene CCR5.

The CCR5 gene encodes a cell-surface chemokine-receptor molecule that serves as a coreceptor for macrophage-tropic strains of HIV-1. Mutations in this gene may alter expression or function of the protein product, thereby altering chemokine binding/signaling or HIV-1 infection of cells that normally express CCR5 protein. Indeed, homozygotes for a 32-bp deletion allele of CCR5 (CCR5-delta 32), which causes a frameshift at amino acid 185, are relatively resistant to HIV-1 infection. Here we report the identification of 16 additional mutations in the coding region of the CCR5 gene, all but 3 of which are codon altering or "nonsynonymous. " Most mutations were rare (found only once or twice in the sample); five were detected exclusively among African Americans, whereas eight were observed only in Caucasians. The mutations included 11 codon-altering nonsynonymous variants, one trinucleotide deletion, one chain-termination mutant, and three synonymous mutations. The high predominance of codon-altering alleles among CCR5 mutants (14/17 [81%], including CCR5-delta 32) is consistent with an adaptive accumulation of function-altering alleles for this gene, perhaps as a consequence of historic selective pressures.