Miracle-dz/UniFAR-FTUs huggingface dataset:
Subtypes of oral carcinoma-associated fibroblasts 1 Identification of two distinct carcinoma-associated fibroblast subtypes with differential tumor-promoting abilities in oral squamous cell carcinoma

1 Identification of two distinct carcinoma-associated fibroblast subtypes with differential tumor-promoting abilities in oral squamous cell carcinoma Daniela Elena Costea, Allison Hills, Amani H. Osman, Johanna Thurlow, Gabriella Kalna, Xiaohong Huang, Claudia Pena Murillo, Himalaya Parajuli, Salwa Suliman, Kulasekara K Keerthi, Anne Chr. Johannessen, and Max Partridge. Section for Pathology, The Gade Institute, University of Bergen, Bergen, Norway. Head and Neck Unit, Guy’s and St. Thomas’ Hospitals NHS Foundation Trust, London, UK. Center for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, UK. 4 Beatson Institute, Glasgow, UK. 5 Institute of Clinical Dentistry, University of Bergen, Bergen, Norway. Department of Pathology, Haukeland University Hospital, Bergen, Norway. Running title: Subtypes of oral carcinoma-associated fibroblasts.
Developing and assessing methods to census and monitor burrow-nesting seabirds in Ireland

1 Chapter 1. General Introduction . 3 1. General Background . 3 2. Manx shearwater (Puffinus puffinus) . 8 3. European storm petrel (Hydrobates pelagicus) . 11 4. Atlantic puffin (Fratercula arctica) . 15 5. Thesis aims and structure . 19 Chapter 2. Sampling strategies for species with high breeding-site fidelity: a case study in burrow-nesting seabirds . 27
Mathematical modelling of airflow in the glottal region and its comparison with experimental data

Finite element method (FEM) was used for numerical simulation of the airflow field in a simplified model of the human vocal tract for vowel /a:/ with prescribed periodic oscillations of the vocal folds. The viscous fluid is modeled by 2D compressible Navier-Stokes equations in Arbitrary LagrangianEulerian (ALE) formulation and considering the turbulence. The computed flow field pattern is compared with the original experimental results obtained by Particle Image Velocimetry (PIV) method.
Defining an Essence of Structure Determining Residue Contacts in Proteins

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this “structural essence” has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts—such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed “cone-peeling” that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 Å Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This “structural essence” opens new avenues in the fields of structure prediction, empirical potentials and docking.
Stabilities of HIV-1 DIS type RNA loop–loop interactions in vitro and in vivo

RNA loop–loop interactions are a prevalent motif in the formation of tertiary structure and are well suited to trigger molecular recognition between RNA molecules. We determined the stabilities of several loop–loop interactions with a constant 6 bp core sequence and varying unpaired flanking nucleotides and found that the flanking bases have a strong influence on the stability and ion dependence of the kissing complex. In general, the stabilities determined in 1 M Na+ are equivalent to those in the presence of near physiological Mg2+ concentrations. Therefore we further tested whether the stabilities determined in vitro and within yeast cells correlate, using a recently developed yeast RNA-hybrid system. For the majority of the loop types analyzed here, the melting temperatures determined in vitro are in good agreement with the relative β-galactosidase activity in yeast cells, showing that data derived from in vitro measurements reflect in vivo properties. The most stable interactions are the naturally occurring HIV-1 DIS MAL and LAI derived loops with the motif (5′ AA/GN6A 3′), emphasizing the crucial role of stable kissing complexes in HIV genome dimerization.
Additive effects of heating and exercise on baroreflex control of heart rate in healthy males.

This study assessed the additive effects of passive heating and exercise on cardiac baroreflex sensitivity (cBRS) and heart rate variability (HRV). Twelve healthy young men (25 ± 1 yr, 23.8 ± 0.5 kg/m2) randomly underwent two experimental sessions: heat stress (HS; whole body heat stress using a tube-lined suit to increase core temperature by ~1°C) and normothermia (NT). Each session was composed of a preintervention rest (REST1); HS or NT interventions; postintervention rest (REST2); and 14 min of cycling exercise [7 min at 40%HRreserve (EX1) and 7 min at 60%HRreserve (EX2)]. Heart rate and finger blood pressure were continuously recorded. cBRS was assessed using the sequence (cBRSSEQ) and transfer function (cBRSTF) methods. HRV was assessed using the indexes standard deviation of RR intervals (SDNN) and root mean square of successive RR intervals (RMSSD). cBRS and HRV were not different between sessions during EX1 and EX2 (i.e., matched heart rate conditions: EX1 = 116 ± 3 vs. 114 ± 3 and EX2 = 143 ± 4 vs. 142 ± 3 beats/min but different workloads: EX1 = 50 ± 9 vs. 114 ± 8 and EX2 = 106 ± 10 vs. 165 ± 8 W; for HS and NT, respectively; P < 0.01). However, when comparing EX1 of NT with EX2 of HS (i.e., matched workload conditions but with different heart rates), cBRS and HRV were significantly reduced in HS (cBRSSEQ = 1.6 ± 0.3 vs. 0.6 ± 0.1 ms/mmHg, P < 0.01; SDNN = 2.3 ± 0.1 vs. 1.3 ± 0.2 ms, P < 0.01). In conclusion, in conditions matched by HR, the addition of heat stress to exercise does not affect cBRS and HRV. Alternatively, in workload-matched conditions, the addition of heat to exercise results in reduced cBRS and HRV compared with exercise in normothermia. NEW & NOTEWORTHY The present study assessed cardiac baroreflex sensitivity during the combination of heat and exercise stresses. This is the first study to show that prior whole body passive heating reduces cardiac baroreflex sensitivity and autonomic modulation of heart rate during exercise. These findings contribute to the better understanding of the role of thermoregulation on cardiovascular regulation during exercise.
MicroRNAs and mesenchymal stem cells: hope for pulmonary hypertension

Pulmonary hypertension is a devastating and refractory disease and there is no cure for this disease. Recently, microRNAs and mesenchymal stem cells emerged as novel methods to treat pulmonary hypertension. More than 20 kinds of microRNAs may participate in the process of pulmonary hypertension. It seems microRNAs or mesenchymal stem cells can ameliorate some symptoms of pulmonary hypertension in animals and even improve heart and lung function during pulmonary hypertension. Nevertheless, the relationship between mesenchymal stem cells, microRNAs and pulmonary hypertension is not clear. And the mechanisms underlying their function still need to be investigated. In this study we review the recent findings in mesenchymal stem cells - and microRNAs-based pulmonary hypertension treatment, focusing on the potential role of microRNAs regulated mesenchymal stem cells in pulmonary hypertension and the role of exosomes between mesenchymal stem cells and pulmonary hypertension.
A multistep linear prediction approach to blind asynchronous CDMA channel estimation and equalization

A multistep linear prediction approach is presented for blind channel estimation and detection of asynchronous short-code DS-CDMA (direct sequence code division multiple access) signals in multipath channels. Only the spreading code of the desired user is assumed to be known; its transmission delay may be unknown. We exploit the previously proposed multistep linear prediction (MSLP) approach for blind multiple-input multiple-output (MIMO) channel estimation in conjunction with the structure imposed by the desired user's spreading code sequence. With the knowledge of the desired user's code sequence, only the second-order statistics of the data are needed under certain sufficient conditions on the underlying multiuser MIMO transfer function. An illustrative simulation example is provided.
Effects of Tylosin on Bacterial Mucolysis, Clostridium perfringens Colonization, and Intestinal Barrier Function in a Chick Model of Necrotic Enteritis

ABSTRACT Necrotic enteritis (NE) is a worldwide poultry disease caused by the alpha toxin-producing bacterium Clostridium perfringens. Disease risk factors include concurrent coccidial infection and the dietary use of cereal grains high in nonstarch polysaccharides (NSP), such as wheat, barley, rye, and oats. Outbreaks of NE can be prevented or treated by the use of in-feed antibiotics. However, the current debate regarding the prophylactic use of antibiotics in animal diets necessitates a better understanding of factors that influence intestinal colonization by C. perfringens as well as the pathophysiological consequences of its growth. We report a study with a chick model of NE, which used molecular (16S rRNA gene [16S rDNA]) and culture-based microbiological techniques to investigate the impact of the macrolide antibiotic tylosin phosphate (100 ppm) and a dietary NSP (pectin) on the community structure of the small intestinal microbiota relative to colonization by C. perfringens. The effects of tylosin and pectin on mucolytic activity of the microbiota and C. perfringens colonization and their relationship to pathological indices of NE were of particular interest. The data demonstrate that tylosin reduced the percentage of mucolytic bacteria in general and the concentration of C. perfringens in particular, and these responses correlated in a temporal fashion with a reduction in the occurrence of NE lesions and an improvement in barrier function. The presence of pectin did not significantly affect the variables measured. Thus, it appears that tylosin can control NE through its modulation of C. perfringens colonization and the mucolytic activity of the intestinal microbiota.
Hypoxia promotes the production and inhibits the destruction of human articular cartilage.

OBJECTIVE To determine the effects of hypoxia on both anabolic and catabolic pathways of metabolism in human articular cartilage and to elucidate the roles played by hypoxia-inducible factors (HIFs) in these responses. METHODS Normal human articular cartilage from a range of donors was obtained at the time of above-the-knee amputations due to sarcomas not involving the joint space. Fresh cartilage tissue explants and isolated cells were subjected to hypoxia and treatment with interleukin-1α. Cell transfections were performed on isolated human chondrocytes. RESULTS Using chromatin immunoprecipitation, we found that hypoxia induced cartilage production in human tissue explants through direct binding of HIF-2α to a specific site in the master-regulator gene SOX9. Importantly, hypoxia also suppressed spontaneous and induced destruction of human cartilage in explant culture. We found that anticatabolic responses were predominantly mediated by HIF-1α. Manipulation of the hypoxia-sensing pathway through depletion of HIF-targeting prolyl hydroxylase-containing protein 2 (PHD-2) further enhanced cartilage responses as compared to hypoxia alone. Hypoxic regulation of tissue-specific metabolism similar to that in human cartilage was observed in pig, but not mouse, cartilage. CONCLUSION We found that resident chondrocytes in human cartilage are exquisitely adapted to hypoxia and use it to regulate tissue-specific metabolism. Our data revealed that while fundamental regulators, such as SOX9, are key molecules both in mice and humans, the way in which they are controlled can differ. This is all the more important since it is upstream regulators such as this that need to be directly targeted for therapeutic benefit. HIF-specific hydroxylase PHD-2 may represent a relevant target for cartilage repair.
Within- and Among-Family Variation in Parasite Load and Parasite-Induced Mortality in the Land Snail Arianta arbustorum, a Host of Parasitic Mites

Abstract Variation in host susceptibility and parasite-induced mortality are preconditions for parasite-related selection on host populations. In terrestrial gastropods, variation in resistance against ectoparasite infection is poorly understood. We examined the within- and among-family variation in parasite load in full-siblings of the land snail Arianta arbustorum experimentally infected with Riccardoella limacum, a mite living in the mantle cavity of helicid land snails. We also quantified the influence of family origin and host size on parasite load and calculated its heritability (h2). Furthermore, we examined the influence of parasite load, snail size, and family origin on host winter mortality, an important life-history trait of A. arbustorum. Parasite load was heritable (h2 = 0.63). In infected snails, parasite load was affected by family origin and increased with increasing shell size. Host mortality during hibernation increased with increasing parasite load and differed among families, but was not affected by snail size. Our results show high among-family variation both in resistance against ectoparasite infection and in host winter mortality. Furthermore, we show that parasite load is linked to snail size, which suggests that the proliferation of R. limacum is limited by resources provided by A. arbustorum.
Effects of Environmental Context on Physiological Response During Team Handball Small Sided Games

This study examined the distance covered and physiological effects of altering the number of players during small-sided games (SSG) in team handball. Twelve professional female handball players [24.6±3.7 years, 172±6.2 cm, 68.2 ± 9.9kg, 22.7 ± 2 kg/m2] participated in this study. The SSG were played, first with five on each side (SSG 5), then four (SSG 4), then three (SSG 3). Each game was four minutes long, followed by three minutes of rest. The distance covered and time spent in four speed zones (based on player movement speed) were selected for analysis: Zone 1 (0–1.4 m/s), Zone 2 (1.5–3.4 m/s), Zone 3 (3.5–5.2 m/s), and Zone 4 (>5.2 m/s). Statistically significant differences were found in Zone 2, between conditions SSG 3 and SSG 4 (p=.049,ω2= .32). The highest average heart rate (HR) occurred during SSG 3. Average HR between SSG 3 (89.7 % HRmax) and SSG 5 (87.8 % HRmax) (p= .04, ω2= .26) were also significantly different. Participant HR response between the speed zones was not statistically significant. HR response was negatively correlated with the number of players within the SSG condition. Statistically significant results were found for RPE between SSG 3 and the other two SSG conditions (SSG 4, p = .01, and SSG 5, p = .00). These results indicate that changing the number of SSG players can be used to manipulate the physiological response during handball training.
Superficial Hemangioma: Pulsed Dye Laser Versus Wait‐and‐See

Background and Objectives Childhood hemangioma is the most common soft tissue tumor of infancy, occurring in 10% of children younger than 1 year old. Ten percent of these infantile hemangiomas involute yearly without intervention. Treatment with the pulsed dye laser (PDL) is the criterion standard for treating vascular lesions. It is well established as the most effective, safest treatment for port‐wine stains. Previous studies of the use of PDL treatment in superficial hemangioma showed inconsistent results. Main objectives were to compare the efficacy and adverse effects of PDL treatment with those of observation in the treatment of superficial hemangiomas. Parental quality of life was also assessed. Materials and Methods This was a prospective, randomized, controlled trial in which we enrolled 22 infants aged 1.5 to 5 months old with early hemangiomas with a maximum diameter of 5 cm. We assigned the infants to PDL treatment (n = 11) or observation (n = 11), and followed up until the age of 1 year. Patients in the intervention group were treated using a 595‐nm PDL (VBEAM, Candela Corp., Wayland, MA) with a 7‐mm spot diameter, 30/10 to 40/10‐ms epidermal cooling, a 7‐ to 15‐J/cm2 fluence range, and a pulse duration of 0.45 to 40.0 ms. During follow‐up, color measurements were made (Colori meter; Minolta, Tokyo, Japan), and surface area and echo depth of the hemangioma were determined. Results No significant differences were seen between the groups at time of inclusion or at the age of 1 year in echo depth (p = .66) or surface area (p = .62). Results were significant for color difference (p = .03) between PDL treatment and observation. Cosmetic outcome judged by an independent panel consisting of a dermatologist, physician assistant, dermatology resident, dermatology nurse, and plastic surgery resident was significantly better in the PDL treatment group (46%) than in the observation group (18%) (p = .006). Conclusions Pulsed dye laser is only to be considered as an alternative treatment up to the age of 6 months, at which time parents and physicians consider cosmetic outcome to be a relevant factor, but laser therapy plays a major role in the treatment of residual lesions at older ages.
Optimal Sum Rate of the MIMO Relay Communication System

For a class of the important problems that seek to maximize the sum rate of the multiple input multiple output relay communication system (MIMO RCS) and compute the optimal transmission distributions, we present their mathematical models, and then develop an efficient algorithm for solving this class of the problems. The fixed point theory is used to prove convergence of the proposed algorithm. The performance result of the proposed new algorithm indicates that the proposed algorithm overcomes some limitations of other algorithms. First it utilizes the machinery of parallel computation, a limitation of the previously known iterative water-filling algorithms. Second it is robust to the large number of users $K$, as the previously known iterative water-filling algorithms are not. Not only does the proposed algorithm sufficiently utilize the machinery of parallel computation, but it also shows a strong robustness for the number of the users $K$. At the same time, the proposed algorithm shows fast convergence.
Seek, and ye shall find: Differences between spontaneous and voluntary analogical retrieval

The present study tackles two overlooked aspects of analogical retrieval: (a) whether argumentation activities elicit a spontaneous search for analogical sources, and (b) whether strategic search can relax the superficial bias typically obtained in experimental studies of analogical retrieval. In Experiment 1, participants had to generate arguments for a target situation under three conditions: without indication to use analogies, with indication to use analogies, and with indication to search for sources within domains provided by the experimenters. Results showed that while voluntary search yields analogical retrievals reliably, the argumentation activity seldom elicits spontaneous remindings. A second set of results demonstrated that the superficial bias can be strategically relaxed, leading to a majority of distant retrievals. Experiment 2 replicated this result with the instruction to search within domains different from that of the target, and without providing a list of specific domains. The theoretical and educational implications of these findings are discussed.
A Review of Histiocytic Diseases of Dogs and Cats

Histiocytic proliferative disorders are commonly observed in dogs and less often cats. Histiocytic disorders occur in most of the dendritic cell (DC) lineages. Canine cutaneous histiocytoma originates from Langerhans cells (LCs) indicated by expression of CD1a, CD11c/CD18, and E-cadherin. When histiocytomas occur as multiple lesions in skin with optional metastasis to lymph nodes and internal organs, the disease resembles cutaneous Langerhans cell histiocytosis of humans. Langerhans cell disorders do not occur in feline skin. Feline pulmonary LCH has been recognized as a cause of respiratory failure due to diffuse pulmonary infiltration by histiocytes, which express CD18 and E-cadherin and contain Birbeck’s granules. In dogs and cats, histiocytic sarcomas (HS) arise from interstitial DCs that occur in most tissues of the body. Histiocytic sarcomas begin as localized lesions, which rapidly disseminate to many organs. Primary sites include spleen, lung, skin, brain (meninges), lymph node, bone marrow, and synovial tissues of limbs. An indolent form of localized HS, progressive histiocytosis, originates in the skin of cats. Hemophagocytic HS originates in splenic red pulp and bone marrow macrophages in dogs and cats. In dogs, histiocytes in hemophagocytic HS express CD11d/CD18, which is a leuko-integrin highly expressed by macrophages in splenic red pulp and bone marrow. Canine reactive histiocytic diseases, systemic histiocytosis (SH) and cutaneous histiocytosis, are complex inflammatory diseases with underlying immune dysregulation. The lesions are dominated by activated interstitial DCs and lymphocytes, which invade vessel walls and extend as vasocentric infiltrates in skin, lymph nodes, and internal organs (SH).
Medical ultrasound: imaging of soft tissue strain and elasticity

After X-radiography, ultrasound is now the most common of all the medical imaging technologies. For millennia, manual palpation has been used to assist in diagnosis, but it is subjective and restricted to larger and more superficial structures. Following an introduction to the subject of elasticity, the elasticity of biological soft tissues is discussed and published data are presented. The basic physical principles of pulse-echo and Doppler ultrasonic techniques are explained. The history of ultrasonic imaging of soft tissue strain and elasticity is summarized, together with a brief critique of previously published reviews. The relevant techniques—low-frequency vibration, step, freehand and physiological displacement, and radiation force (displacement, impulse, shear wave and acoustic emission)—are described. Tissue-mimicking materials are indispensible for the assessment of these techniques and their characteristics are reported. Emerging clinical applications in breast disease, cardiology, dermatology, gastroenterology, gynaecology, minimally invasive surgery, musculoskeletal studies, radiotherapy, tissue engineering, urology and vascular disease are critically discussed. It is concluded that ultrasonic imaging of soft tissue strain and elasticity is now sufficiently well developed to have clinical utility. The potential for further research is examined and it is anticipated that the technology will become a powerful mainstream investigative tool.