Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying Transcriptional Dynamics and Their Effects on Genetic Motifs from Live Cell Fluorescence Microscopy

Advances in measurement techniques based on fluorescent tagging have enabled visualizing individual transcripts and proteins over time as they are produced in live cells. Such methods are critical in understanding how genes and genetic networks function, how they respond to external signals, such as stress conditions and temperature changes, and how cellular aging and diseases can affect their performance. This is relevant, as the functioning of genes and genetic networks affects the survival of cells and cell populations. However, as cellular processes are complex and inherently stochastic, statistical signal processing methods are required to pre-process, analyze, and interpret the results from the measurement data. This stems from various traits of the data: averages poorly describe the behavior of multimodal populations; confidence estimates and hypothesis testing must be used to compare results, as they feature significant variability; and large data sets are required such that comparison can be made with sufficient confidence, rendering manual quantification excessively laborious. In addition, when combined with stochastic models, such methods can be used to extract information, which cannot be directly measured with current techniques. Meanwhile, the methods must be carefully designed, in order to avoid hidden assumptions which obstruct the objective quantification and comparison of the results. Finally, the methods should be made robust against errors characteristic to the measurement system or propagating from the earlier stages of the analysis. Here, methods were developed in order to enhance the amount and the quality of the information which can be extracted from single-molecule measurements of live cells. In particular, methods for estimating RNA numbers and RNA production intervals from static images of cell populations and from time series of images of growing cells were first established. Next, methods for estimating the subprocesses of transcription were developed, as these processes cannot be directly measured in live cells. Computer simulations and live single-RNA measurements were used to demonstrate the reliability and performance of the new methods, indicating that the methods can adapt to different measurement settings and can be applied to other similar dynamical estimation problems. Finally, computer simulations of genetic networks are used to demonstrate that the accuracy of such methods is
Effects of exotic genotypes and genetic backgrounds on fiber quality and plant architectural traits in Upland cotton (Gossypium hirsutum L.)

30 Introduction . 30 Materials and methods . 32 Results . 35 Discussion . 42 Conclusion . 44 References . 45 3. ASSOCIATION OF MICROSATELLITE MARKERS WITH YIELD RELATED AND PLANT ARCHITECTURAL TRAITS IN UPLAND COTTON . 60 Abstract . 61. 6
Prooxidant effects of melatonin: a brief review

Melatonin acts classically through the widely expressed G protein-coupled membrane receptors MT1 and MT2, respectively. The functional role of the MT receptors is not fully clear with multiple effects, such as effects on the circadian, reproductive, immune, cardiovascular, and intestinal systems, being suggested. In addition to receptor-mediated effects, melatonin also acts as a potent antioxidant and it is quite evident that melatonin and its metabolites efficiently reduce oxidative damage to proteins, lipids, and DNA and also exert protective effects on mitochondria. The potent antioxidant activity of melatonin stems from various complex mechanisms, including direct scavenging of radicals, stimulation of antioxidant enzymes, and maintenance of mitochondrial homeostasis. However, about a dozen experimental studies also suggest that melatonin can exert prooxidant effects under certain circumstances. Involvement of calmodulin and the mitochondrial respiratory chain may be potential targets for the prooxidant effects of melatonin. This review briefly summarizes the physiobiochemistry of melatonin, including its antioxidative functions, and summarizes and discusses studies showing prooxidant effects of this hormone.
Size at maturity for grooved Tanner crab (Chionoecetes tanneri) along the U.S. west coast (Washington to California)

We conducted a multiyear study to examine interannual variability in the mean size (carapace width, mm), maturity size (mm) and depth (m) for grooved Tanner crab (Chionoecetes tanneri (Rathbun, 1893)) along the U.S. west coast. An additional goal was to provide updated estimates of carapace width (mm) at 50% maturity (W50) for male and female grooved Tanner crab and assess changes over time. Randomly selected samples came from trawl surveys undertaken annually by the Northwest Fisheries Science Center at depths of 55 to 1280 m. We used allometric relationships between carapace width (CW) and either abdominal width (AW) (females) or chela length (CL) (males) to determine functional maturity by sex. We evaluated maturity by fitting logistic regression models to proportion mature grooved Tanner crab. W50 varied significantly between males (125.2 mm) and females (89.1 mm) but interannual differences were slight. The annual mean CW were greater for mature males (139.9–143.4 mm) relative to females (98.8–100.4 mm). The average sizes of immature grooved Tanner crab varied between sexes with males (75.7–84.6 mm) larger than females (66.7–71.9 mm). Size frequency distributions indicated little overlap in the size of mature male and female grooved Tanner crab but considerable overlap between immature grooved Tanner crab. The best model expressing complexity in growth incorporated width, sex and maturity stage. Depth ranged from 195–1254 m with the average depth of a mature grooved Tanner crab (females, 737 m; males, 767 m) significantly shallower than an immature (females, 949 m; males, 918 m) grooved Tanner crab.
Effect of post-hatch feed deprivation on growth, immune organ development and immune competence in broiler chickens.

The effect of post hatch feed deprivation on growth, immune organ development and immune competence was studied in broiler chickens. A total of 240 broiler chicks hatched with in a period of 8h were transported to the rearing site with in 30 minutes of hatch. The body weight of chicks (41.33±0.24 g) were measured individually and randomly distributed into 4 groups of 60 chicks each with 6 replicates in each group. The treatments included accessed to feed at 0, 12, 24 and 48h post hatching. All the chicks were reared in battery brooder cages under uniform managemental conditions. The body weight gain during 0-7, 0-21 and 0-42 d were significantly lower in the chicks those were deprived of for 48h of hatch compared to the other groups. Feed conversion ratio and mortality was not affected by the duration of post hatch feed deprivation. The development of both bursa and spleen, and cell mediated (LPR) and humoral (SRBC and ND tires) immune responses were affected due to feed deprivation during initial 24h of hatch. Feed deprivation for more duration i.e. 48h after hatch further reduced the immune response. The findings of the present study thus suggested that feed deprivation for 48h after hatch had negative effect on growth; however, feed deprivation for 24h had adverse effect on development of immune system as well as immune competence in broilers.
Mood disorders, sleep and circadian rhythms

Sleep disturbances and disruptions of circadian rhythms are underlying factors in most mood disorders like major depressive disorder (MDD) and bipolar disorder (BD), and their seasonal pattern or seasonal affective disorder (SAD). Decreases in sleep efficiency, total sleep time and sleep quality have all been documented in MDD. In addition to this, depressed patients of all these three categories (MDD, BD, SAD) exhibit profound disturbances in circadian rhythms including the sleep-wake rhythm. Circadian clock dysregulation has been suggested to be due abnormal circadian rhythmicity of gene expression. In particular, CRY1 and CRY2 polymorphisms have been shown to be associated with MDD. Similarly, variations in CRY2, PER2, ARNTL and NPAS2 are associated with SAD. An antidepressant that benefits sleep quality and resynchronize disrupted circadian rhythms will be most useful in treating mood disorders. In this context, the newly introduced melatonergic antidepressant agomelatine with MT1 and MT2 agonistic properties with 5HT2C antagonism has been documented to be beneficial, as it improves sleep, resynchronizes the disrupted circadian rhythms, and elevates mood. This drug also manifests with fewer adverse effects and is emerging as an effective an-
Chronic cadmium toxicity in rats: Treatment with combined administration of vitamins, amino acids, antioxidants and essential metals

The present study was designed to investigate the protective effect of dietary nutrients against cadmium-induced hepatic and renal toxicities in male albino rats. The animals were randomly divided into eleven groups where the control group (Group Ⅰ) received physiological saline (p.o.) and Group Ⅱ was administered with cadmium chloride (2 mg/kg, s.c.) only. Groups Ⅲ, Ⅳ, Ⅴ, Ⅵ, Ⅶ, Ⅷ and IX received 10 mg/kg dietary nutrients, i.e. thiamine, methionine, N-acetylcysteine (NAC), melatonin, zinc (Zn), vitamin E and cystine, respectively. Group Ⅹ received a dose of 0.1 mg/kg of selenium (Se) and Group Ⅺ was administered with a combination of NAC, Zn, vitamin B1 and melatonin. All treatments were administered orally for 21 days with a concomitant subcutaneous (s.c.) cadmium treatment. Cadmium-intoxicated rats exhibited hepatic and renal toxicities as indicated by elevation of lipid peroxidation and marked decline in superoxide dismutase, glutathione peroxidase, alkaline phosphatase activities and total protein. However, a combined treatment with dietary nutrients, i.e. methionine, zinc, vitamin B1 and N-acetylcysteine ameliorated cadmium-induced lipid peroxidation and oxidative stress as they provoked the antioxidant defense system more significantly, when compared to each of them alone and hence is suggested as protective against cadmium-induced hepatic and renal toxicities.
Effect of Natto-feeding on Cholesterol Levels of Rats

コレステロール (Chl) 負荷および非負荷条件下で, 飼料中へ納豆5～10%レベルの添加が, ラットの成長, 臓器重量, 各組織Chlに及ぼす影響について検討した。 同たん白レベルでの体重増加には影響がなかった。 肝重量はChl負荷で増加したが, 飼育期間の延長に伴い納豆添加により増加が抑制された。 盲腸重量は納豆添加により増加した。 血清総Chlは, 8日間飼育したときには, 納豆10%添加によりChl負荷による上昇が抑制された。 肝ChlはChl負荷で著しく増加したが, 納豆による抑制効果は認められなかった。
Five new species of Leioproctus (Protomorpha) Rayment (Hymenoptera: Colletidae)

Five new species of Leioproctus (Protomorpha) Rayment from western Queensland are described: Leioproctus crispus n.sp. , L. gibber n.sp. , L. gurneyi n.sp. , L. latifrons n.sp. and L. nix n.sp. Females of all the new species, except L. nix, have specialized setae on the clypeus, frons or vertex of the head. A revised key to species is provided. Batley, Michael, and Tony J. Popic. 2013. Five new species of Leioproctus (Protomorpha) Rayment (Hymenoptera: Colletidae). Records of the Australian Museum 65(2): 39–50.
Correction

COLLOQUIUM Correction for “Challenges in constraining anthropogenic aerosol effects on cloud radiative forcing using present-day spatiotemporal variability,” by Steven Ghan, Minghuai Wang, Shipeng Zhang, Sylvaine Ferrachat, Andrew Gettelman, Jan Griesfeller, Zak Kipling, Ulrike Lohmann, Hugh Morrison, David Neubauer, Daniel G. Partridge, Philip Stier, Toshihiko Takemura, Hailong Wang, and Kai Zhang, which appeared in issue 21, May 24, 2016, of Proc Natl Acad Sci USA (113:5804–5811; first published February 26, 2016; 10.1073/pnas.1514036113). The authors note the order of affiliations for Minghuai Wang appeared incorrectly: this author’s first affiliation should be listed as Institute for Climate and Global Change Research, Nanjing University. The corrected author and affiliation lines appear below. The online version has been corrected. The authors also note that, due to a printer’s error, Eq. 3 appeared incorrectly. The corrected equation appears below. The online version has been corrected.
Taxonomic status of Velinoides Matsumura (Hemiptera: Reduviidae: Harpactorinae) inferred from mitochondrial and nuclear genes

In this study, we used three mitochondrial genes (cyt b, COI, and 16S rRNA) and one nuclear gene (28S rRNA) to evaluate the current taxonomic status of the genus Velinoides erected by Matsumura. Phylogenetic analyses of genes using maximum parsimony, maximum likelihood, and minimum evolution resulted in different phylogenetic trees. However, the combined dataset analysis revealed better phylogenetic relationships. The constructed phylogenies appeared to be largely congruent with morphological studies. Results based on the molecular data strongly supported that the C. dilatatus, the type species of Velinoides, was the sister group to all other species of the genus Coranus Curtis. Incorporation with the morphological and cytogenetic characteristics, we proposed that Velinoides is of subgeneric status, the genus Coranus Curtis should be divided into two subgenera, Velinoides Matsumura and Coranus Curtis. Our phylogenetic results suggested that the 28S rDNA gene segment alone might not be an optimal molecular marker for the phylogeny of the genus Coranus Curtis.
Morpho-physiological attributes of three HYV aromatic fine rice varieties as affected by integrated nutrient management

An experiment was conducted at the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh to study the morpho-physiological attributes of three HYV aromatic fine rice varieties as affected by integrated nutrient management. The experiment comprised three aromatic fine rice varieties viz. BRRI dhan34, BRRI dhan37 and BRRI dhan38; and eight nutrient managements viz. control (no manures and fertilizers), recommended dose of inorganic fertilizers, cowdung at 10 t ha , poultry manure at 5 t ha, 50% of recommended dose of inorganic fertilizers + 50% cowdung, 50% of recommended dose of inorganic fertilizers + 50% poultry manure, 75% of recommended dose of inorganic fertilizers + 50% cowdung and 75% of recommended dose of inorganic fertilizers + 50% poultry manure. The experiment was laid out in a randomized complete block design with three replications . BRRI dhan34 produced the tallest plant (115.8cm) at 85 DAT whereas the highest number of total tillers hill(14.56) was found at 70 DAT in the same variety. The highest leaf area index (LAI) (5.431) and the highest amount of total dry matter (TDM) production hill (49.47 g hill) were found at 70 DAT in BRRI dhan34. Crop growth rate (CGR) (30.47 g m day) was found highest at 55-70 DAT in BRRI dhan34.On the other hand, application of 75% of recommended dose of inorganic fertilizers + 50% cowdung resulted in the highest plant height (123.3 cm) at 85 DAT, the highest number of total tillers hill (15.57) and the highest LAI (6.050) at 70 DAT, the highest amount of TDM accumulation (59.91 g hill) at 85 DAT and the highest CGR (41.65 g m day) at 55-70 DAT. The interaction effect between BRRI dhan34 and 75% of recommended dose of inorganic fertilizers + 50% cowdung produced the tallest plant (127.0 cm) at 85 DAT, the highest number of total tillers hill (16.2) and the highest LAI (6.4) at 70 DAT and the highest CGR (46.96 g m day) at 55-70 DAT. Grain yield showed significantly positive correlation with leaf area index (r = 0.929**) and total dry matter production (r = 0.948**) at 70 DAT.
Cloning and expression of glutathione peroxidase 2 gene in rapeseed(Brassica napus L.)

In order to investigate the role of glutathione peroxidase(GPX) gene in rapeseed(Brassica napus L.) under abiotic stress,the BnGPX2 gene cDNA was cloned from rapeseed variety Ningyou16 by RT-PCR.It was 644 bp in full length,and its open reading frame was 510 bp in length,which encoded a 169 amino acids sequence with isoelectric point of 5.6 and molecular mass of 18 960.The deduced protein sequence was very similar(92.3%) to the GPX2 of Arabidopsis thaliana,and had three characteristic domains of plant GPXs and three conserved Cys residues through alignment of the whole amino acid sequences of some known GPXs.The genomic DNA fragment of BnGPX2 gene was isolated by common PCR method,being 1 782 bp in full length.Sequence analysis of the genomic fragment demonstrated that the gene consisted of six exons and five introns,and all the introns were spliced following the consensus sequence,having GT and AG at their 5′and 3′ends,respectively.Expression analysis of the BnGPX2 in rapeseed tissues was performed by semi-quantitative RT-PCR,and different patterns were detected under different abiotic stresses.The results showed that the BnGPX2 was constitutively and ubiquitously expressed,with high levels in root,stem,leaf or flower,and low in silique.The expressions of BnGPX2 increased under drought or water logging stress.However,it did not respond to the salt,high temperature or cold stress.
Essential Oil Percentage of Celery and Parsley and Their Components As Affected By Method Extraction

Medicinal and aromatic plants often used as natural medicines because of their remedial properties. Product of plant origin has become an exciting area of research in drug discovery and development. Medicinal and aromatic plants mainly exploited for essential oil extraction for many applications in industries. This study aims to evaluate two extraction methods on essential oil percentage and components of celery and parsley seeds. Celery essential oil percentage gave insignificant effect according to the two used methods, meanwhile parsley essential oil percentage appeared significant values, and the main components of the two plants decreased with extracted by evaporator, (limonene of celery and Myristicin of parsley). Limonene was decreased from 71.32% with hydro distillation to 42.04% with evaporator hydro distillation, myristicin was lower from 77.58% to 53.69% according to the previously methods. Monoterpene hydrocarbons decreased in two plants with evaporator hydro distillation, but oxygenated compounds were increased and the decrease was very low in both two plants, meanwhile sesquiterpene hydrocarbons cleared decrease in celery and increase in parsley. According to previously, recommended by application the two methods (hydroditilation of water and evaporator) for essential oil extraction of both of celery and parsley seeds.
Spatial Variability of Rock Depth using Artificial Intelligence Techniques

This study describes two Artificial Intelligence (AI) techniques for predicting spatial variability of rock depth in Bangalore. Reduced level of rock (d) at Bangalore, India is arrived from the 652 boreholes data in the area covering 220 km 2 . The first AI technique uses generalized regression neural network (GRNN) that are trained with suitable spread(s) to predict d at any point in Bangalore. The second technique uses Least Square Support Vector Machine (LSSVM), is a statistical learning theory which adopts a least squares linear system as a loss function instead of the quadratic program in original support vector machine (SVM). Here, LSSVM has been used as a regression technique. A comparative study between the two developed AI techniques has been presented in this paper. The results indicate that the developed GRNN model has the ability to predict d with an acceptable degree of accuracy {Coefficient of Correlation(r) =0.885, and Root Mean Square Error (RMSE) =0.021}. Whereas, the developed LSSVM model predicts d with an acceptable degree of accuracy (r =0.967, and RMSE=0.004). This study also highlights the capability of LSSVM model over GRNN.
New records of exotic spiders and insects to the Azores, and new data on recently introduced species

The introduction of exotic species in islands is recognized as a major threat to native biota and ecosystems. In this contribution we list thirteen widespread exotic invertebrate species (two Araneae, one Orthoptera, four Hemiptera, four Coleoptera and two Diptera) that were recorded from the Azorean Islands in the last few years for the first time. In addition, we list another ten invertebrate species (two Araneae, one Orthoptera, two Phasmatodea, one Hemiptera, three Coleoptera and one Diptera) that expanded their known range in the archipelago. The pathways of entrance for species in the Azores, their impact on the local economy and biodiversity, as well as strategies to halt the introduction of alien species are discussed.
On the occurrence of the cirriped barnacle, Chelonibia patula (Ranzani) on the sea snake,Hydrophis cyanocintus (Daudin)

It is reported that a sea snake Hydrophis cyanocintus (Daudin) was found attached with 21 numbers of barnacles Chelonibia patula (Ranzani) on its body. The sea snake collected from the trawler catches landed at Rameswaram was in moulted condition.
In reply: Circumcision for phimosis and other medical indications in Western Australian boys

TO THE EDITOR: Spilsbury et al argue that “improve education or physicians, and perhaps parents, with regard to foreskin development and management is required. ”1 However, updating of textbooks and medical curricula is required to accomplish this objective. Articles by Caldamone et al2 and Cendron et al are two examples of incorrect data in text books. Gairdner was the first to provide data on the normal development of the foreskin in young boys.4 Gairdner incorrectly believed that 92% of boys would have a retractile prepuce by age 5 years. Unfortunately, Gairdner’s data was wrong.5 Gairdner achieved his artificially high rate of retractability by first “running a probe around the preputial space” to break the normal physiological fusion between the foreskin and glans penis,4 a procedure few would recommend today because of pain, trauma, risk of infection, and iatrogenic creation of adhesions. As stated above, some textbooks continue to uncritically parrot Gairdner’s incorrect data. The error has been further compounded by the confusing presentation of data in Øster’s otherwise excellent study.6 Øster presents information about the incidence of “phimosis”, “tight foreskin”, and “adhesions” in separate tables. To obtain the percentage of boys in each age group with partially or completely non-retractile foreskins, it is necessary to sum the percentage incidence of these conditions. When that is done, Øster’s data are very similar to those provided by Kayaba et al7 on the development of the retractile prepuce. Therefore, according to current research, about 50% of boys will have a retractile prepuce by age 10 years and about 99% will have a retractile prepuce by the completion of puberty. The non-retractile foreskin is normal in boys and no cause for concern. Based on the data of Øster6 and Kayaba et al,7 Doctors Opposing Circumcision believes that the new rule-ofthumb should be that about 50% of boys will have a retractile prepuce by age 10 and about 99% will have a retractile prepuce by the completion of puberty. This information needs to be incorporated into textbooks, medical curricula, and information provided to the public. When the normal development of the prepuce is properly understood, one can easily see that patiently awaiting the natural development of preputial retractability will usually eliminate the need for medical or surgical intervention. Better information about the normal development of the foreskin should relieve parental anxiety and reduce false diagnoses of phimosis in boys.
FLUORIDATION OF SYDNEY'S WATER SUPPLY

BINGHAM, E. C. , and ROEPKE, R. R. (1944), "The Rheology of Blood", J. gen. Physiol. , 28 : 79, 131. BIZZOZERO, J. (1882), "Ober einen neuen Fo,. ,nbestandteil des Blutee un,l dessen Rolle bei der Thrombose unter del' Btutoerininmo", Virchows Arch. path. Anat. , 90 : 26l. BLOCH, E. H. , POWELL, A. , MERYMAN, H. T. , WARNER, L. , and KAFIG, E. (1956), "A Comparison of the Surfaces of Human Erythrocytes from Health and Disease by in Vivo Light Microscopy and in Vitro Electron Microscopy", Angiology, 7 : 479.