Miracle-dz/UniFAR-FTUs huggingface dataset:
Wild Skylarks Seasonally Modulate Energy Budgets but Maintain Energetically Costly Inflammatory Immune Responses throughout the Annual Cycle

A central hypothesis of ecological immunology is that immune defences are traded off against competing physiological and behavioural processes. During energetically demanding periods, birds are predicted to switch from expensive inflammatory responses to less costly immune responses. Acute phase responses (APRs) are a particularly costly form of immune defence, and, hence, seasonal modulations in APRs are expected. Yet, hypotheses about APR modulation remain untested in free-living organisms throughout a complete annual cycle. We studied seasonal modulations in the APRs and in the energy budgets of skylarks Alauda arvensis, a partial migrant bird from temperate zones that experiences substantial ecological changes during its annual cycle. We characterized throughout the annual cycle changes in their energy budgets by measuring basal metabolic rate (BMR) and body mass. We quantified APRs by measuring the effects of a lipopolysaccharide injection on metabolic rate, body mass, body temperature, and concentrations of glucose and ketone. Body mass and BMR were lowest during breeding, highest during winter and intermediate during spring migration, moult and autumn migration. Despite this variation in energy budgets, the magnitude of the APR, as measured by all variables, was similar in all annual cycle stages. Thus, while we find evidence that some annual cycle stages are relatively more energetically constrained, we find no support for the hypothesis that during these annual cycle stages birds compromise an immune defence that is itself energetically costly. We suggest that the ability to mount an APR may be so essential to survival in every annual cycle stage that skylarks do not trade off this costly form of defence with other annual cycle demands.
In Vitro and In Vivo Short-Term Pulmonary Toxicity of Differently Sized Colloidal Amorphous SiO2

In vitro prediction of inflammatory lung effects of well-dispersed nanomaterials is challenging. Here, the in vitro effects of four colloidal amorphous SiO2 nanomaterials that differed only by their primary particle size (9, 15, 30, and 55 nm) were analyzed using the rat NR8383 alveolar macrophage (AM) assay. Data were compared to effects of single doses of 15 nm and 55 nm SiO2 intratracheally instilled in rat lungs. In vitro, all four elicited the release of concentration-dependent lactate dehydrogenase, β-glucuronidase, and tumor necrosis factor alpha, and the two smaller materials also released H2O2. All effects were size-dependent. Since the colloidal SiO2 remained well-dispersed in serum-free in vitro conditions, effective particle concentrations reaching the cells were estimated using different models. Evaluating the effective concentration–based in vitro effects using the Decision-making framework for the grouping and testing of nanomaterials, all four nanomaterials were assigned as “active. ” This assignment and the size dependency of effects were consistent with the outcomes of intratracheal instillation studies and available short-term rat inhalation data for 15 nm SiO2. The study confirms the applicability of the NR8383 AM assay to assessing colloidal SiO2 but underlines the need to estimate and consider the effective concentration of such well-dispersed test materials.
Low Levels of Human HIP14 Are Sufficient to Rescue Neuropathological, Behavioural, and Enzymatic Defects Due to Loss of Murine HIP14 in Hip14−/− Mice

Huntingtin Interacting Protein 14 (HIP14) is a palmitoyl acyl transferase (PAT) that was first identified due to altered interaction with mutant huntingtin, the protein responsible for Huntington Disease (HD). HIP14 palmitoylates a specific set of neuronal substrates critical at the synapse, and downregulation of HIP14 by siRNA in vitro results in increased cell death in neurons. We previously reported that mice lacking murine Hip14 (Hip14−/−) share features of HD. In the current study, we have generated human HIP14 BAC transgenic mice and crossed them to the Hip14−/− model in order to confirm that the defects seen in Hip14−/− mice are in fact due to loss of Hip14. In addition, we sought to determine whether human HIP14 can provide functional compensation for loss of murine Hip14. We demonstrate that despite a relative low level of expression, as assessed via Western blot, BAC-derived human HIP14 compensates for deficits in neuropathology, behavior, and PAT enzyme function seen in the Hip14−/− model. Our findings yield important insights into HIP14 function in vivo.
Detection of Spina Bifida by First Trimester Screening – Results of the Prospective Multicenter Berlin IT-Study

Abstract Purpose To evaluate the potential of routine assessment of intracranial translucency (IT) and other posterior brain parameters in the early detection of open spina bifida during the 11 – 14 weeks screening examination. Materials and Methods This prospective, multicenter longitudinal study was conducted with the participation of 20 certified DEGUM II or III experts in Berlin, Germany, between June 2010 and October 2013. All pregnant women undergoing a first trimester screening were included in the study and in every patient were the IT, brain stem (BS), cisterna magna (CM), BS to occipital bone distance (BSOB) and BS/BSOB ratio measured. All patients with continuing pregnancy underwent a second trimester scan. Our data was used to develop our own reference ranges. The primary outcome parameter was the presence of open spina bifida. Results A total of 15 526 women with 16 164 fetuses were examined. Median of the IT was 2.1 mm, of the CM 1.6 mm, of the BS 2.7 mm, of the BSOB 5.5 mm, and of the BS/BSOB ratio 0.49. There were 11 cases with open spina bifida (incidence of 6.8/10 000). The detection rate was 100 % and in all cases of spina bifida, the anomaly was detected either at the first examination (n = 8) or considered suspicious and the lesion then detected a few weeks later (n = 3). Considering individual measurements, however, the detection rate was 18 % with the complete absence of the IT and 45 % with cut-off values. For the CM measurement, the detection rate was 64 % with the absence of the CM and 73 % with cut-off values. The other parameters proved not to be predictive of open spina bifida. Conclusion In the hands of an expert, open spina bifida can be reliably diagnosed early in gestation during the 11 – 14 weeks screening. The measurement of different parameters of the posterior brain, especially the CM and the use of cut-off values are of tremendous benefit in achieving a high sensitivity in the detection rate.
Differential Influence on Cytotoxic T Lymphocyte Epitope Presentation by Controlled Expression of Either Proteasome Immunosubunits or Pa28

The proteasome is the principal provider of major histocompatibility complex (MHC) class I–presented peptides. Interferon (IFN)-γ induces expression of three catalytically active proteasome subunits (LMP2, LMP7, and MECL-1) and the proteasome-associated activator PA28. These molecules are thought to optimize the generation of MHC class I–presented peptides. However, known information on their contribution in vivo is very limited. Here, we examined the antigen processing of two murine leukemia virus-encoded cytotoxic T lymphocyte (CTL) epitopes in murine cell lines equipped with a tetracycline-controlled, IFN-γ–independent expression system. We thus were able to segregate the role of the immunosubunits from the role of PA28. The presence of either immunosubunits or PA28 did not alter the presentation of a subdominant murine leukemia virus (MuLV)-derived CTL epitope. However, the presentation of the immunodominant MuLV-derived epitope was markedly enhanced upon induction of each of these two sets of genes. Thus, the IFN-γ–inducible proteasome subunits and PA28 can independently enhance antigen presentation of some CTL epitopes. Our data show that tetracycline-regulated expression of PA28 increases CTL epitope generation without affecting the 20S proteasome composition or half-life. The differential effect of these IFN-γ–inducible proteins on MHC class I processing may have a decisive influence on the quality of the CTL immune response.
Thyroid hormones and menstrual cycle function in a longitudinal cohort of premenopausal women

BACKGROUND Previous studies have reported that hyperthyroid and hypothyroid women experience menstrual irregularities more often compared with euthyroid women, but reasons for this are not well-understood and studies on thyroid hormones among euthyroid women are lacking. In a prospective cohort study of euthyroid women, this study characterised the relationship between thyroid hormone concentrations and prospectively collected menstrual function outcomes. METHODS Between 2004-2014, 86 euthyroid premenopausal women not lactating or taking hormonal medications participated in a study measuring menstrual function. Serum thyroid hormones were measured before the menstrual function study began. Women then collected first morning urine voids and completed daily bleeding diaries every day for three cycles. Urinary oestrogen and progesterone metabolites (estrone 3-glucuronide (E1 3G) and pregnanediol 3-glucuronide (Pd3G)) and follicle-stimulating hormone were measured and adjusted for creatinine (Cr). RESULTS Total thyroxine (T4 ) concentrations were positively associated with Pd3G and E1 3G. Women with higher (vs lower) T4 had greater luteal phase maximum Pd3G (Pd3G = 11.7 μg/mg Cr for women with high T4 vs Pd3G = 9.5 and 8.1 μg/mg Cr for women with medium and low T4 , respectively) and greater follicular phase maximum E1 3G (E1 3G = 41.7 ng/mg Cr for women with high T4 vs E1 3G = 34.3 and 33.7 ng/mg Cr for women with medium and low T4 , respectively). CONCLUSIONS Circulating thyroid hormone concentrations were associated with subtle differences in menstrual cycle function outcomes, particularly sex steroid hormone levels in healthy women. Results contribute to the understanding of the relationship between thyroid function and the menstrual cycle, and may have implications for fertility and chronic disease.
Acid activation of Helicobacter pylori vacuolating cytotoxin (VacA) results in toxin internalization by eukaryotic cells

Helicobacter pylori VacA is a secreted toxin that induces multiple structural and functional alterations in eukaryotic cells. Exposure of VacA to either acidic or alkaline pH (‘activation’) results in structural changes in the protein and a marked enhancement of its cell‐vacuolating activity. However, the mechanism by which activation leads to increased cytotoxicity is not well understood. In this study, we analysed the binding and internalization of [125I]‐VacA by HeLa cells. We detected no difference in the binding of untreated and activated [125I]‐VacA to cells. Binding of acid‐activated [125I]‐VacA to cells at 4°C was not saturable, and was only partially inhibited by excess unlabelled toxin. These results suggest that VacA binds either non‐specifically or to an abundant, low‐affinity receptor on HeLa cells. To study internalization of VacA, we used a protease protection assay. Analysis by SDS–PAGE and autoradiography indicated that the intact 87 kDa toxin was internalized in a time‐dependent process at 37°C but not at 4°C. Furthermore, internalization of the intact toxin was detected only if VacA was acid or alkaline activated before being added to cells. The internalization of activated [125I]‐VacA was not substantially inhibited by the presence of excess unlabelled toxin, but was blocked if cells were depleted of cellular ATP by the addition of sodium azide and 2‐deoxy‐d‐glucose. These results indicate that acid or alkaline pH‐induced structural changes in VacA are required for VacA entry into cells, and that internalization of the intact 87 kDa toxin is required for VacA cytotoxicity.
Design and Implementation of Scalable Register Files Using Adiabatic Quantum Flux Parametron Logic

We have been investigating adiabatic quantum flux parametron (AQFP) as a low-power superconductor logic. In this paper, we propose multi-block power distribution and modular design for high- speed and scalable AQFP register files. In the multi-block power distribution, the entire circuit is divided into multiple blocks so as to solve clock skews. In the modular design, bit width can be increased by adding bit slices. We designed and demonstrated an 8-word and 1-bit register file adopting multi-block power distribution.
Complete mitochondrial genome of black-banded trevally (Seriolina nigrofasciata): Genome characterization and phylogenetic considerations

Abstract The black-banded trevally (Seriolina nigrofasciata) is a species of the family Carangidae and the only known member of genus Seriolina. To understand the phylogenetic relationship of black-banded trevally in teleost, we first determined the complete mitochondrial genome of black-banded trevally. The entire mitochondrial genome of black-banded trevally is 16 531 bp in length, containing 13 protein-coding genes and 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNAs), and 2 main non-coding regions. The overall base composition is T 25.8%, C 30.0%, A 26.7%, and G 17.5%. The gene arrangement, base composition, and tRNA structures of black-banded trevally are consistent with those of other teleost. Two of the central conserved sequence blocks (CSB-2 and CSB-3) were identified and the core sequence (TACATGTATGTA) of terminal-associated sequences was recognized in the control region. Meanwhile, the conserved motif 5′-GCCGG-3′ was identified in the origin of light-strand replication of black-banded trevally. The complete mitochondrial genome of black-banded trevally was used to construct phylogenetic tree, which shows that black-banded trevally is clustered with the fishes of the genus Seriola. We expect that the availability of the mitochondrial genome of black-banded trevally will facilitate the further investigations of molecular systematic and phylogenetic analysis of the Carangidae.
The epidemiological evidence behind the association between periodontitis and incident atherosclerotic cardiovascular disease.

OBJECTIVES The objective of this study was to systematically review the epidemiological evidence for an association between periodontitis (PD) and incident atherosclerotic cardiovascular disease (ACVD), including coronary heart disease (CHD), cerebrovascular disease and peripheral arterial disease. METHODS Systematic review of cohort and case-control studies on the association of clinically or radiographically diagnosed PD and ACVD. RESULTS Overall, 12 studies were included in this study (six studies on CHD, three studies on cerebrovascular disease, two studies on both coronary heart and cerebrovascular disease mortality and one study on peripheral arterial disease). All but one study reported positive associations between various periodontal disease measures and the incidence of ACVD, at least in specific subgroups. The association was stronger in younger adults and there was no evidence for an association between PD and incident CHD in subjects older than 65 years. Only one study evaluated the association between PD and secondary cardiovascular events. CONCLUSIONS There is evidence for an increased risk of ACVD in patients with PD compared to patients without. However, this may not apply to all groups of the population. There is insufficient evidence for an association between PD and the incidence of secondary cardiovascular events.
Complete mitochondrial genome of Sebastes owstoni (Scorpaenidae, Scorpaeniformes) from the East Sea, Korea

Abstract Sebastes owstoni is a popular fishery species in the north-western Pacific Ocean. To obtain basic information on its mitochondrial DNA (mtDNA), the complete mitogenome of S. owstoni was subjected to the next-generation sequencing. The assembled mtDNA was 16,465 bp in length, comprising 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and a control region. The complete mitogenome comprised of 27.7% A, 26.6% T, 17.3% G and 28.4% C, indicating a slight AT bias (54.3%). The start codon of all PCGs was ATG, with the exception of COX1 (GTG). The stop codons in the PCGs were mainly TAA, with the exception of ND1 and ND3 (TAG), ND4 (AGA) and Cytb (incomplete termination codon, T). All tRNAs had a typical cloverleaf shape, with the exception of tRNASer (AGY), which lacked the DHU arm. The sequenced mitogenome of S. owstoni can be used in genetics-based management initiatives or for constructing the mitochondrial lineages within Scorpaenidae.
Robust H-infinity tracking control of MIMO nonlinear systems. Application to non-isothermal CSTR

A non-isothermal Continuous Stirred Tank Reactor (CSTR) is the most important element of chemical industrial equipment which exhibits a highly nonlinear behavior. It is one of multi-input multi-output (MIMO) nonlinear systems affected by disturbances. The operation of the non-isothermal CSTR is disturbed by external factors such as changes in the inlet concentration and temperature. Therefore, the two difficult issues in CSTR control are tracking trajectory and external disturbance attenuation. In this paper, a robust fuzzy tracking control via Takagi-Sugeno (T-S) MIMO systems is designed to robustly stabilize the non-isothermal CSTR system for both concentration and temperature schemes exposed to external disturbances. Takagi-Sugeno fuzzy approach for describing nonlinear model with several local linear models is proposed, and using a technique called Parallel Distributed Compensation (PDC), we derive LMI conditions for analyzing robust stability and performance based on Lyapunov functions, and a criterion is employed to guarantee the attenuation of disturbances. In trajectory tracking framework, an integral action is introduced as a new state variable. Finally, simulation results are given to prove that the proposed technique ensures the stability conditions and guarantees robustness against external disturbance with a good trajectory tracking.
Post-Conflict Affiliation by Chimpanzees with Aggressors: Other-Oriented versus Selfish Political Strategy

Consolation, i.e., post-conflict affiliation directed from bystanders to recent victims of aggression, has recently acquired an important role in the debate about empathy in great apes. Although similar contacts have been also described for aggressors, i.e., appeasement, they have received far less attention and their function and underlying mechanisms remain largely unknown. An exceptionally large database of spontaneous conflict and post-conflict interactions in two outdoor-housed groups of chimpanzees lends support to the notion that affiliation toward aggressors reduces the latter's aggressive tendencies in that further aggression was less frequent after the occurrence of the affiliation. However, bystander affiliation toward aggressors occurred disproportionally between individuals that were socially close (i.e., affiliation partners) which suggest that it did not function to protect the actor itself against redirected aggression. Contrary to consolation behavior, it was provided most often by adult males and directed toward high ranking males, whereas females engaged less often in this behavior both as actors and recipients, suggesting that affiliation with aggressors is unlikely to be a reaction to the distress of others. We propose that bystander affiliation toward aggressors may function to strengthen bonds between valuable partners, probably as part of political strategies. Our findings also suggest that this post-conflict behavior may act as an alternative to reconciliation, i.e., post-conflict affiliation between opponents, in that it is more common when opponents fail to reconcile.
Simulation of the mild wear of cams in valve trains under mixed lubrication

Cam–follower kinematic pairs in the valve trains of engines usually operate in the mixed lubrication regime and work under conditions of wear. The wear mode of cams in mixed lubricated contacts is mild, and the wear value is usually calculated using Archard’s equation in which the wear coefficient is closely related to the lubrication condition. In this study, a nonlinear relationship between the wear coefficient and lubricant oil film thickness under mixed lubrication is proposed with consideration of the rough height distribution of the contact surface. As the cam and flat tappet pair of the valve train in a diesel engine is concerned, the wear coefficient of the cam material for boundary lubrication conditions is measured. After calculating the lubricant oil thickness, the wear depths at different points of the cam are simulated, and results are consistent with the measured values in the practical test.
Laparoscopic staging of gastrointestinal tumours.

management of those problems. Only with a complete knowledge of the staging of the disease can the appropriate treatment be applied, be it surgical or medical. Many of the approaches for this pre-operative (or “non operative”) staging are based in imaging exams that have shown, up till now, some degree of failure in its results. This is due to a lack of definition, both in dimensions and in histology. The technical characteristics of the equipment have seen a constant improvement but we are still far from having these definitions given only by imaging. Although laparoscopic US was first mentioned in 1963 (1), the first reference to the use of laparoscopy for staging is from 1971 (2). In 1986, some more interest was shown and it started, as well, to show some diagnostic superiority (3) The rationale for staging is based in the knowledge of the correct TNM stage. Obtaining in due time adequate information that would allow the application of the most appropriate therapy does this. On the other hand, we can also obtain a better prognosis for the situation; a correct staging allows R0 resections with a supposedly more appropriate management of the situation. This also offers better QoL for the patient, avoiding more aggressive procedures, eventually unnecessary, and giving some shortening in the hospital length of stay. Over-staged tumours have under-treatment by having a management which is not aggressive enough or is not even applied; on the other hand, under-staged tumours will have over-treatment, with too many non-radical surgeries being performed or with patients undergoing unnecessary laparotomies. Another question has to do with the laparoscopic approach. Why shall it be laparoscopic? Several factors are already well known enough as to justify this: It is less aggressive and allows better management of QoL, also diminishing post-operative pain and discomfort; early identification of eventual lesions non visualized during the pre-op staging is possible in an easy way and a more adequate management of diagnosis and therapeutic measures is achieved, allowing at the same time the execution of palliative procedures. It is necessary to have perfectly clarified the notion that none of these attitudes goes without a very thorough workout of the usual steps in patient diagnosis: clinical history, laboratory and observation data, imaging exams, endoscopies, CT scans and MNRs, trans-abdominal and endoscopic ultrasonographies, scintigraphies and FDG-PET, as well as other exams are mandatory to have the overview of the patient as complete as possible, before going to the surgical staging. With a carefully applied surgical technique, delicate and often lengthy, always with the use of