Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of CBCT-based image guidance for a large cohort of lung cancer patients treated with SABR

This study evaluates respiratory excursions and their impact on patient setup and dosimetric coverage with and without the use of cone-beam computed tomography (CBCT) for localization in stereotactic ablative radiotherapy. The datasets of 150 non-small cell lung cancer patients were assessed. Four groups of patients were evaluated based on their tumor location: upper lobe (UL)-peripheral (N = 39), UL-chest-wall seated (CWS, N = 37), lower lobe (LL)-peripheral (N = 48), and LL-CWS (N = 26). Tumor excursion and setup error were quantified and correlated. Treatment planning margins were derived based on the van Herk formalism. A dosimetric study investigated the dose coverage with and without the use of CBCT for localization. The percentage of patients showing >5 mm tumor respiratory excursion for UL-peripheral/LL-peripheral was 10.0/42.9%, and was 4.2/46.7% for UL-CWS/LL-CWS. Planning margin magnitudes averaged over all patients were Mresidual(2.7, 3.2, 3.7) mm and Minterfxn(9.0, 14.0, 10.0) mm, respectively with and without the use of CBCT for image guidance. Comparatively, the planning margins for the patients with LL tumors exhibiting the largest motion and setup errors were MresidualLL(2.8, 3.6, 4.4). Pearson correlation coefficients (for LL-peripheral tumors in the S/I direction) between tumor excursion and, respectively, inter-fraction and residual setup errors were 0.62 and 0.32. Based on skin tattoo setup, the overall average difference in D95 dose to the planning target volume (PTV) between the delivered and planned doses was 14.1 ± 9.2%. The use of CBCT for localization reduced the overall average ΔD95 to less than 2%. This analysis is suggestive that: (a) patients with LL tumors undergo the largest respiratory-induced motion, and experience larger setup errors relative to UL tumors; (b) the use of CBCT-based image guidance significantly reduces residual setup errors; planning margins of the order of 5 mm appear to be adequate for proper PTV dose coverage; (c) CBCT image guidance reduces the correlation between respiratory-induced motion and setup errors, implying that there is much less variation in the setup uncertainty between tumors undergoing respiratory motion of varying magnitudes, relative to the variation without CBCT.
Sexually transmitted infections: unravelling transmission & impact

The aim of the thesis was to gain insight into sexual mixing patterns, the effect of these patterns on the spread of sexually transmitted infections (STIs), pathogen interactions, and infectious disease progression and outcome. The main findings are: 1. Among heterosexuals in Amsterdam, partnership factors (e.g. age difference) are more important determinants of unprotected sexual contact than characteristics of the individual. STI prevalence differences between ethnic populations are not always caused by differences in sexual behaviour. 2. Demographic characteristics (e.g. age) are less important for partner selection among men who have sex with men (MSM); the key determinant of unprotected anal intercourse among MSM is perceived concordant HIV status. Molecular epidemiology of Chlamydia trachomatis and N. gonorrhoeae did not reveal subpopulations among MSM, suggesting a homogeneously mixed population, but the risk to acquire N. gonorrhoeae differed between meeting venues. Furthermore, the pharynx is more important for the spread of N. gonorrhoeae than the rectum, even though the prevalence of rectal infections is higher. 3. The disease burden of hepatitis C virus infection will increase in the upcoming years among people who inject drugs. HCV treatment will reduce the burden, but postponing implementation of treatment reduces its effect, because the population becomes older and the average duration of infection is increasing. 4. Finally, no evidence for a reduction in mortality from HIV-1 in individuals dually infected with HIV-1 and HIV-2 in West Africa was found. We are entering a new era in which biomedical prevention strategies become important. In response, pathogen dynamics are likely to change.
Effect of Hydroculture Methods on Tomato Root Morphology and Anatomy

Three methods of hydroculture were compared for their effects on the root anatomy and morphology of tomato ( Solanum lycopersicum cv. Defiant ). A hydroponic deep water culture method, an ebb-flood system using expanded clay pellets as a solid medium and an aeroponic sub-mist system were compared, with a solid peat/perlite medium for control. The treatments were found to have significant effects on plant root and shoot length, as well as root and shoot biomass. Root morphology was visually distinct among treatments, and all methods of hydroculture were associated with a significant increase in vascular tissue in plant roots compared with the control. Root hairs were also visible on plants grown in ebb-flood systems. Plants grown in peat/perlite medium tended to show reduced root and shoot biomass compared with the treatment. These data seem to corroborate the connection between hydroculture and increased plant growth rate. Additionally, they suggest that greater water availability leads to increased diameter of vascular structures in roots, and that root hair development is influenced by aeration and media texture
Follistatin gene therapy for the treatment of muscular dystrophy.

ii Dedication . iv Acknowledgements . v Vita . vi List of Tables . xi List of Figures . xii Chapter 1: Overview . 1 Chapter 2: Background Early Descriptions of Muscular Dystrophy . 5 Muscle Structure . 8 Common Clinically Defined MDs . 10 Current MD Therapies . 17 Emergent Treatment Strategies for MD . 19 Myostatin Inhibition for Enhanced Muscle Growth . 23 Follistatin for Myostatin Inhibition . 27 Gene Therapy for Follistatin Administration . 30 Figures.34 Tables . 41 viii Chapter 3: Methods Mice . 42 Non-Human Primates . 42 Construction of AAV1 and Self-Complimentary AAV9 Expressing Follistatin.43 Viral Vector Production . 43 Mouse Injections . 44 Mouse Behavioral Testing.45 Grip Strength . 45 Coordination . 45 Ambulatory Movements and Rearing Events . 45 Mouse Survival . 46 Non-Human Primate Injections . 46 Non-Human Primate Muscle Physiology . 47 Serum Creatine Kinase Assay . 48 Follistatin Enzyme-Linked ImmunoSorbent Assay . 48 Non-Human Primate Immune Studies . 49 Muscle Histology . 50 Fat Tissue Analysis . 50 Muscle Fiber Size Histogram . 51 Production of Recombinant Follistatin . 51 Binding of Follistatin to Laminin-1 and Merosin (Laminin-α2) . 51 Microarray . 52 Statistics . 53 ix Chapter 4: Single Administration of AAV1-Follistatin-344 Enhances Muscle Mass and Strength in mdx Mice Introduction . 54 Results . 57 Discussion . 60 Figures . 64 Chapter 5: AAV1-Follistatin Enhances Muscle Mass and Function in Non-Human Primates Introduction . 67 Results . 70 Discussion . 73 Figures . 77 Chapter 6: Follistatin Gene Therapy Improves Symptoms in a Severe Mouse Model of Congenital Muscular Dystrophy Introduction . 80 Results . 84 Discussion . 91 Figures . 97 Tables . 105 Chapter 7: Possible Follistatin Mediated Interactions that Promote Muscle Growth and Enhancement Introduction . 107 Results . 110 Muscle Growth and Hypertrophy . 112 Muscle Development and Stability.113 Muscle Pathology.114 x Discussion . 115 Figures.117 Tables . 119 Chapter 8: Discussion . 121 References . 129
Pine invasion decreases density and changes native tree communities in woodland Cerrado

ABSTRACT Background: Invasive plants can negatively impact native communities, but the majority of the effects of these invasions have been demonstrated only for temperate ecosystems. Tropical ecosystems, including the Cerrado, a biodiversity hotspot, are known to be invaded by numerous non-native species, but studies of their impacts are largely lacking. Aims: Our research aimed at quantifying how Pinus spp. presence and density affected Cerrado plant communities. Methods: We sampled areas invaded and non-invaded by Pinus spp. to determine if pine invasion affected native tree richness, diversity, evenness, and density. We also evaluated if community composition differed between invaded and non-invaded sites. Results: We found invaded plots had lower native tree densities than non-invaded plots and that Pinus spp. invasions changed native tree communities by reducing native species abundances. Conclusion: Invasive pines had negative impacts on the native Cerrado tree community by reducing native plant density and changing species abundances. Reduced density and abundance at early invasion stages can result in reduction in biodiversity in the long term.
ZCWPW1 is recruited to recombination hotspots by PRDM9, and is essential for meiotic double strand break repair

During meiosis, homologous chromosomes pair (synapse) and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, recombination initiates with double-strand breaks (DSBs) within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have yet been identified. We identified Zcwpw1, which possesses H3K4me3 and H3K36me3 recognition domains, as highly co-expressed with Prdm9. Here, we show that ZCWPW1 has co-evolved with PRDM9 and, in human cells, is strongly and specifically recruited to PRDM9 binding sites, with higher affinity than sites possessing H3K4me3 alone. Surprisingly, ZCWPW1 also recognizes CpG dinucleotides, including within many Alu transposons. Male Zcwpw1 homozygous knockout mice show completely normal DSB positioning, but persistent DMC1 foci at many hotspots, particularly those more strongly bound by PRDM9, severe DSB repair and synapsis defects, and downstream sterility. Our findings suggest a model where ZCWPW1 recognition of PRDM9-bound sites on either the homologous, or broken, chromosome is critical for synapsis, and hence fertility. Graphical Abstract Legend In humans and other species, recombination is initiated by double strand breaks at sites bound by PRDM9. Upon binding, PRDM9 deposits the histone marks H3K4me3 and H3K36me, but the functional importance of these marks has remained unknown. Here, we show that PRDM9 recruits ZCWPW1, a reader of both these marks, to its binding sites genome-wide. ZCWPW1 does not help position the breaks themselves, but is essential for their downstream repair and chromosome pairing, and ultimately meiotic success and fertility in mice.
Çukurova Üniversitesi Yerleşkesinde Artan Yapılaşmanın Floraya Etkisinin Belirlenmesi

Turlerin korunmasi amaciyla dunyada kabul gormus birincil strateji korunan alanlarin ilanidir. Bu kategorilerin disinda devlet kurumlarinin bulundugu alanlar ya da Cukurova Universitesinde oldugu gibi, universite yerleskeleri de biyolojik cesitliligin korundugu/korunabilecegi onemli alanlardir. Arastirma alanini olusturan Cukurova Universitesi Yerleskesi, 1 977.26 hektarlik bir alani kapsamaktadir. Bu alan zengin biyolojik cesitlilige sahip olmasina ragmen, artan yapilasma sureci tehdidi altindadir. Bu gercekten hareketle calismanin amaci, Cukurova Universitesi Yerleskesinde artan egitim ogretim dokusu kapsamindaki yapilasmalarin flora uzerine etkilerinin belirlenmesidir. Amaci dogrultusunda arastirmada ilk olarak yerleskenin 1987 yili ile 2018 yili alan kullanimlari ArcGIS 10.0 bilgisayar yazilimi ile siniflandirilmistir. Arazi calismalari kapsaminda elde edilen veriler dogrultusunda bitkiler, oncelikle Raunkiaer’in hayat formlarina gore siniflandirilmis, yerleskede endemizm orani saptanmis ve daha sonra yerleskenin antropojenik degisim derecesi saptanmistir. Basta endemik turler olmak uzere bircok bitki turu icin habitat olan alanlarin egitim ogretim dokusu icin yapilasmaya acildigi belirlenmistir.
EFFECT OF PARTURITION ON WHITE BLOOD CELLS COUNT (WBC) AND T CELLS SUBSETS IN SELENIUM SUPPLEMENTED NEWBORN LAMBS

The aim of the work was assessed the influence of parturition at the dynamics of leukocytes and T cells subsets in a selenium supplemented newborn lambs. The experiment was conducted on nineteen sucking newborn lambs of the Sumava sheep breed. After parturition blood samples were taken from lambs on day 10, 30 and 60. The WBC in blood smear was detected by microscopically analysis (norm no. 84 3206), and the CD4 + and CD8 + T cells subsets in blood were detected by flow cytometery. The WBC was in physiological norm. The highest WBC was founded on 30 th day of the experiment. In the dynamics of the CD4 + a CD8 + T cells subsets were founded statistically significant differences: In the CD4 + subset between 10 th and 30 th day of the experiment (P < 0.001) and between 30 th and 60 th day of the experiment (P < 0.01), and in the CD8 + subset between 10 th and 30 th day of the experiment (P < 0.001). Excepted in 30 th day of the experiment were counts of the CD4 + and CD8 + T cells subsets inside the physiological norm.
Emergence of opposite neurons in a firing-rate model of multisensory integration

Opposite neurons, found in macaque dorsal medial superior temporal (MSTd) and ventral intraparietal (VIP) areas, combine visual and vestibular cues of self-motion in opposite ways. A neural circuit recently proposed utilizes opposite neurons to perform causal inference and decide whether the visual and vestibular cues in MSTd and VIP should be integrated or segregated. However, it is unclear how these opposite connections can be formed with biologically realistic learning rules. We propose a network model capable of learning these opposite neurons, using Hebbian and Anti-Hebbian learning rules. The learned neurons are topographically organized and have von Mises-shaped feedforward connections, with tuning properties characteristic of opposite neurons. Our purpose is two-fold: on the one hand, we provide a circuit-level mechanism that explains the properties and formation of opposite neurons; on the other hand, we present a way to extend current theories of multisensory integration to account for appropriate segregation of sensory cues.
Relaciones tróficas y ecotoxicológicas entre los copépodos acartia grani y euterpina acutifrons y diversas especies de dinoflagelados planctónicos marinos

Las proliferaciones de dinoflagelados toxicos pueden producir efectos directos e indirectos sobre la estructura de las diferentes comunidades que componen los ecosistemas marinos. En este sentido, se destaca el efecto de sus toxinas sobre los demas organismos acuaticos y tambien la posibilidad de que estas toxinas sean transferidas a eslabones superiores de la cadena trofica, a traves de los consumidores zooplanctonicos herbivoros. Entre estos ultimos, se destaca el papel ejercido por los copepodos debido a su abundancia y extensa distribucion geografica y tambien por las relaciones troficas que mantienen con especies fitoplanctonicas marinas y dulceacuicolas. En esta memoria se describen diversos, experimentos de alimentacion con los copepodos Acartica grani y Euterpina acutifrons, que fueron realizados con la finalidad de determinar las tasas de ingestion y de supervivencia de estos organismos, cuando fueron expuestos a distintas concentraciones de los dinoflagelados toxicos Alexandrium minutum (clones AL1V, AL2V y AMINAR1), Gyrodinium corsicum y Gymnodinium catenatum. Como controles no toxicos se utilizaron las algas Rhodomonas baltica, Prorocentrum triestinum y Scrippsiella trochoidea. Por otro lado, el empleo de tecnicas de cromatografia liquida de alta eficacia con deteccion fluorimetrica (CLAE-DF/HPLC-FC), propicio el descubrimiento de una nueva especie productora de toxinas PSP, Gyrodinim corsicum. La capacidad de ingerir celulas toxicas, observadas tanto en A.grani como en C.acutrifrons, nos permite concluir que ambas especies pueden ser consideradas como vectores potenciales de toxinas PSP dentro de las cadenas troficas marinas, aunque en diferente grado. Acartia grani demostro una mayor capacidad de retencion de toxinas y consecuentemente una mayor toxicidad total en sus tejidos comparada con Euterpina acutrifrons. Por otra parte, esto no indica que su potencial vectorial sea superior al de E.acutri
Effects of chlorogenic acid on the liver cell metabolism under high glucose conditions

This work aimed to investigate the potential of chlorogenic acid (CGA) to modulate the response of human hepatocytes under hyperglycemic condition. Markers of oxidative stress such as reduced glutathione content, malondialdehyde levels, advanced oxidation protein products, and nitric oxide production, as well as protein expression of Nrf2 transcription factor were measured in HepG2 cells cultured in normoglycemic (5.55 mM) and high-glucose medium (25 and 35 mM) preand post-treated with different concentrations of CGA (5, 10, 50 μM). Our results brought evidence of the protective effect of CGA on hepatic cells under hyperglycemic conditions that act through modulation of the intracellular reduced glutathione content and Nrf2 protein expression. The efficiency of CGA was more pronounced in the pre-treatment experiment. The findings of the present investigation demonstrated the protective role of CGA on hepatocytes by attenuating some markers of hyperglycemiamediated oxidative stress.
Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex

The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation 1–4. Metazoan γ-TuRCs isolate as ∼2 MDa complexes containing the conserved proteins γ-tubulin, GCP2 and GCP3, as well as the expanded subunits GCP4, GCP5, and GCP6 3,5,6. However, in current structural models, γ-TuRCs assemble solely from subcomplexes of γ-tubulin, GCP2 and GCP3 7. The role of the metazoan-specific subunits in γ-TuRC assembly and architecture are not currently known, due to a lack of high resolution structural data for the native complex. Here, we present a cryo-EM structure of the native human γ-TuRC at 3. 8Å resolution. Our reconstruction reveals an asymmetric, single helical-turn and cone-shaped structure built from at least 34 polypeptides. Pseudo-atomic models indicate that GCP4, GCP5 and GCP6 form distinct Y-shaped assemblies that structurally mimic GCP2/GCP3 subcomplexes and are distal to the γ-TuRC “seam”. Evolutionary expansion in metazoan-specific subunits diversifies the γ-TuRC by introducing large (>100,000 Å2) surfaces that could interact with different regulatory factors. We also identify an unanticipated structural bridge that includes an actin-like protein and spans the γ-TuRC lumen. Despite its asymmetric composition and architecture, the human γ-TuRC arranges γ-tubulins into a helical geometry poised to nucleate microtubules. The observed compositional complexity of the γ-TuRC could self-regulate its assembly into a cone-shaped structure to control microtubule formation across diverse contexts, e.g. within biological condensates 8 or alongside existing filaments 9.
Influence of rootstocks GF677 and GXN 15 (Garnem) on some phenophases of peach cultivars.

The influence of the peach-almond hybrid rootstocks GF 677 and GXN 15 (Garnem) on the flowering, fruit ripening and the end of vegetation phenophases were studied for the Redhaven, UFO 4 peach cultivars and Big Top nectarine cultivar over a period of three years. It was found that the rootstock GXN 15 (Garnem) induced the onset of flowering up to two days earlier in all cultivars throughout the study period, whereas the rootstock GF 677 increased the flowering duration. Our results demonstrate that both rootstocks do not induce differences in the fruit ripening and end of vegetation periods. Furthermore, the Big Top cultivar tends toward earlier development at the end of winter which makes it highly sensitive to late spring frost.
Hypomagnesemia in dairy cattle in Uruguay

ABSTRACT: An outbreak of hypomagnesemia is reported in Holstein dairy cattle grazing lush oat (Avena sativa) pasture in Uruguay. Nine of 270 (3.3%) cows died in May-July (autumn-winter) 2017. These nine cows were from 2 to 9-years-old (1st-6th lactation), with 22 to 194 days of lactation and 15.8 to 31.4L of daily milk production. Two cows with acute sialorrhea, muscle spasms, lateral recumbency, weakness, opisthotonos, and coma, were euthanized and necropsied. No significant macroscopic or histological lesions were found. One untreated clinically-affected cow and eight out of 14 clinically healthy cows of the same group under similar management and production conditions had low serum levels of Mg (lower than 0.7mmol/L). Secondarily, both clinically affected cows and six out of 14 healthy cows had low serum Ca levels. The K/(Ca+Mg) ratio of two oat forages, corn silage, and ration was 5.10, 7.73, 2.45, and 0.85, respectively. A K/(Ca+Mg) ratio lower than 2.2 represents a risk for hypomagnesemia. The difference between the contribution-requirement of minerals in the diet was established and a daily deficiency of Mg (-0.36g/day), Na (-25.2g/day) and Ca (-9.27g/day) was found, while K (184.42g/day) and P (12.81g/day) were in excess. The diet was reformulated to correct the deficiencies and the disease was controlled by the daily administration of 80g of magnesium oxide, 80g of calcium carbonate and 30g sodium chloride per cow. It is concluded that hypomagnesemia is a cause of mortality in dairy cattle in Uruguay, and that the condition can be prevented by appropriate diet formulation.
Social Support and Self-care Behavior among Heart Failure Patients: Is there any Relationship

Heart failure is one of the main cardiovascular diseases and social support towards it is an important benchmark for accomplishing healthy behavior. The aim of this study was to determine relationship between social support and self-care behavior among heart failure patients. This cross-sectional study was conducted among 64 heart failure patients attending Isfahan Cardiovascular Research Institute during 2013. Data collections were based on standard questionnaires and are analyzed by SPSS version 20 using Pearson's correlation statistical test. The mean age of respondents was 54.5 years (SD: 7.8). There was correlation between social support and self-care behavior (P<0.001 & r=0.481). Furthermore, family support was highly correlated with self-care behaviors (P<0.001 & r=0.462). It seems that it could be beneficial to provide educational programs to patient's families for more support of patients in doing self-care behaviors.
Rod-cone signal interference in the retina shapes perception in primates

Linking the activity of neurons, circuits and synapses to human behavior is a fundamental goal of neuroscience. Meeting this goal is challenging, in part because behavior, particularly perception, often masks the complexity of the underlying neural circuits, and in part because of the significant behavioral differences between primates and animals like mice and flies in which genetic manipulations are relatively common. Here we relate circuit-level processing of rod and cone signals in the non-human primate retina to a known break in the normal seamlessness of human vision – a surprising inability to see high contrast flickering lights under specific conditions. We use electrophysiological recordings and perceptual experiments to identify key mechanisms that shape the retinal integration of rod- and cone-generated retinal signals. We incorporate these mechanistic insights into a predictive model that accurately captures the cancellation of rod- and cone-mediated responses and can explain the perceptual insensitivity to flicker.