Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes – Observing Strong Local Effects of Nucleoid Structure on Gene Regulation

Both intrinsic and extrinsic mechanisms regulating bacterial expression have been elucidated and described, however, such studies have mainly focused on local effects on the two-dimensional structure of the prokaryote genome while long-range as well as spatial interactions influencing gene expression are still only poorly understood. In this paper, we investigate the association between co-expression and distance between genes, using RNA-seq data at multiple growth phases in order to illuminate whether such conserved patterns are an indication of a gene regulatory mechanism relevant for prokaryotic cell proliferation, adaption, and evolution. We observe recurrent sinusoidal patterns in correlation of pairwise expression as function of genomic distance and rule out that these are caused by transcription-induced supercoiling gradients, gene clustering in operons, or association with regulatory transcription factors (TFs). By comparing spatial proximity for pairs of genomic bins with their correlation of pairwise expression, we further observe a high co-expression proportional with the spatial proximity. Based on these observations, we propose that the observed patterns are related to nucleoid structure as a product of transcriptional spilling, where genes actively influence transcription of spatially proximal genes through increases within shared local pools of RNA polymerases (RNAP), and actively spilling transcription onto neighboring genes.
Confinement discerns swarmers from planktonic bacteria

Powered by flagella, many species of bacteria exhibit collective motion on a solid surface commonly known as swarming. Physical changes like cell elongation and hyper flagellation have been shown to accompany swarming phenotype. Less noticeable, however, are the contrasts of collective motion between the swarming cells and the planktonic cells of comparable cell density. Here, we show that when confined by microwells of specific sizes mounted on a soft agar surface, novel bacteria Enterobacter sp. SM3 under swarming condition exhibited “single-swirl” motion pattern distinct from “multi-swirl” motion pattern formed by its concentrated planktonic counterpart. We hypothesize that “rafting behavior” of the swarming bacteria upon dilution might account for the motion pattern difference. This was further validated through computational simulation where swarming cells are modeled by lower repulsion and stronger alignment among them than planktonic cells. Our new technical approach also enabled us to observe swarming on a non-agar tissue surface.
A review of diets in the notaspidea (Mollusca: Opisthobranchia)

This paper reviews the scattered and often anecdotal literature on foods for the opisthobranch order Notaspidea. All Umbraculacea are sponge-feeders (accepting sponges of the class Demospongiae only). The Pleurabranchacea shows a diversity of diet: Berihella species eat sponges (Demospongiae); Berthellina species eat sponges (Demospongiae;? Calcarea) and cnidarians (Scleractinia — not previously reported;? Actiniaria); Pleurobranchus species eat ascidians; Pleurobranchaea (and apparently Pleurobranchella) species are opportunistic carnivores that accept a range of soft-bodied invertebrates (Cnidaria; Annelida; Mollusca). It appears that cnidarians (Actiniaria; Hydroida) are amongst the more preferred items in the diet of Pleurobranchaea species. The review is supplemented with observations on feeding of Berthellina citrina (RUppell & Leuckart) and Pleurobranchaea maculata (Quoy & Gaimard) made at Leigh, New Zealand.
An Approach to Convert Non-Grammatical Words to Grammatical Words to Extract Sentiments using Lexicon Analysis

— we use a lexicon based approach for discovering sentiments. Our lexicon is built from tokenization taxonomy consists of positive, negative, neutral phrases. A typical tweet contains word variations, emoticons, hash tags etc. We use preprocessing steps such as stemming, emoticon detection and normalization, exaggerated word shortening and hash tag detection.
The subthalamic dopamine D5 receptors in Parkinson’s disease

Parkinson’s disease is a neurological disorder characterized by the manifestation of the cardinal motor symptoms, which are attributed to the progressive degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNc). It has been reported that the burst firing is a pathological signature of STN neurons in Parkinson’s disease, however, the origin of bursts remains unknown. Here we tested the hypothesis that dopamine D5 receptors, characterized by a high constitutive activity, may contribute to the emergence of burst firing in the STN and therefore in the manifestation of parkinsonian motor deficits. We tested this hypothesis and have shown that application of an inverse agonist inhibits D5 receptors constitutive activity within the STN and reduced burst firing of STN neurons in brain slices. Moreover, itconverted pathological STN burst firing into physiological tonic activity in the 6-OHDA rat model of Parkinson’s disease. These results are the first to demonstrate that subthalamic D5 receptors are involved in the pathophysiology of Parkinson’s disease and that administering an inverse agonist to these receptors may alleviate motor symptoms.
Molecular and electrophysiological features of spinocerebellar ataxia type seven in induced pluripotent stem cells

Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disease caused by a polyglutamine repeat expansion in the ATXN7 gene. Patients with this disease suffer from a degeneration of their cerebellar Purkinje neurons and retinal photoreceptors that result in a progressive ataxia and loss of vision. As with many neurodegenerative diseases, studies of pathogenesis have been hindered by a lack of disease-relevant models. To this end, we have generated induced pluripotent stem cells (iPSCs) from a cohort of SCA7 patients in South Africa. First, we differentiated the SCA7 affected iPSCs into neurons which showed evidence of a transcriptional phenotype affecting components of STAGA (ATXN7 and KAT2A) and the heat shock protein pathway (DNAJA1 and HSP70). We then performed electrophysiology on the SCA7 iPSC-derived neurons and found that these cells show features of functional aberrations. Lastly, we were able to differentiate the SCA7 iPSCs into retinal photoreceptors that also showed similar transcriptional aberrations to the SCA7 neurons. Our findings demonstrate that iPSC-derived neurons and photoreceptors from SCA7 patients express molecular and electrophysiological differences that are indicative of impaired neuronal health. We hope that these findings will contribute towards the ongoing efforts to establish the cell-derived models of neurodegenerative diseases that are needed to develop patient-specific treatments.
Modelled interglacial carbon cycle dynamics during the Holocene, the Eemian and MIS 11

Trends in the atmospheric concentration of CO2 during three recent interglacials, the Holocene, the Eemian and Marine Isotope Stage (MIS) 11, are investigated using an Earth system Model of Intermediate Complexity, which we extended with process-based modules to consider two slow carbon cycle processes − peat accumulation and shallow-water CaCO3 sedimentation (coral reef formation). For all three interglacials, model simulations considering peat accumulation and 10 shallow water CaCO3 sedimentation substantially improve the agreement between model results and ice core CO2 reconstructions in comparison to a carbon cycle setup neglecting these processes. This enables us to model the trends in atmospheric CO2, with modelled trends similar to the ice core data, forcing the model only with orbital and sea level changes. During the Holocene, anthropogenic CO2 emissions are required to match the observed rise in atmospheric CO2 after 3 ka BP, but are not relevant before this time. Our model experiments show a considerable improvement in the 15 modelled CO2 trends by the inclusion of the slow carbon cycle processes, allowing us to explain the CO2 evolution during the Holocene and two recent interglacials consistently using an identical model setup.
The cryostratigraphy of the Yedoma cliff of Sobo-Sise Island (Lena Delta) reveals permafrost dynamics in the Central Laptev Sea coastal region during the last about 52 ka

The present study examines the formation history and cryolithological properties of late Pleistocene Yedoma Ice Complex (IC) and its Holocene cover in the eastern Lena Delta on Sobo-Sise Island. The sedimentary sequence was continuously sampled in 0.5 m resolution at a vertical Yedoma cliff starting from 24.2 m above rivel level (arl). The 20 sequence differentiates into three cryostratigraphic units; unit A: dated from ca. 52 to 28 cal ka BP; unit B: dated from ca. 28 to 15 cal ka BP; unit C: dated from ca. 7 to 0 cal ka BP. Three chronologic gaps in the record are striking. The hiatus during the interstadial MIS 3 (36–29 cal ka BP) as well as during stadial MIS 2 (20–17 cal ka BP) might be related to fluvial erosion and/or changed discharge patterns of the Lena River caused by repeated outburst floods from the glacial Lake Vitim in Southern Siberia along the Lena River valley towards the Arctic Ocean. The hiatus during the MIS 2-1 transition (15–7 cal 25 ka BP) is a commonly observed feature in permafrost chronologies due to intense thermokarst activity of the deglacial period. The chronologic gaps of the Sobo-Sise Yedoma record are similarly found at two neighbouring Yedoma IC sites on Bykovsky Peninsula and Kurungnakh-Sise Island, and most likely of regional importance. The three cryostratigraphic units of the Sobo-Sise Yedoma exhibit distinct signatures in properties of their clastic, organic and ice components. Higher permafrost aggradation rates of 1 m ka with higher organic matter (OM) stocks (29±15 kg C m 30 , 2.2±1.0 kg N m) and mainly coarse silt are found for the interstadial MIS 3 unit A if compared to the stadial MIS 2 unit B with 0.7 m ka permafrost aggradation, lower OM stocks (14±8 kg C m, 1.4±0.4 kg N m in unit B) and pronounced peaks in the coarse silt and medium sand fractions. Geochemical signatures of intrasedimental ice reflect the differences in summer evaporation and moisture regime by higher ion contents and less depleted stable δO and δD isotope ratios but lower deuterium excess (d) values during interstadial MIS 3 if compared to stadial MIS 2. The δO and δD composition of MIS 3 35 https://doi.org/10.5194/tc-2020-179 Preprint. Discussion started: 24 July 2020 c © Author(s) 2020. CC BY 4.0 License.
Comparing the Effect of Two Promoters on Cassava Somatic Embryo at Transient GUS Assay Level.

35S promoter from the Cauliflower Mosaic Virus (pCaMV) is a constitutive promoter commonly used in plant genetic transformation while Cassava Mosaic Virus (pCsVMV) is another promoter which is underutilized. The combination of the two promoters was used to form (pOYE153). The method adopted includes the insertion of a β–glucuronidase reporter gene (UidA) into a promoter cassette comprising the CsVMV promoter. The second construct (pCAMBIA2310) had (pCaMV) used for the selectable marker and gene of interest. This construct was mobilized into Agrobacterium tumefaciens strain LBA4404 and then tested for expression of the UidA gene in transient assays in cassava somatic embryos. After co-cultivation of these Agrobacterium with the plant tissues, histochemical β–glucuronidase (GUS) assays were performed to determine the level of UidA gene expression in transient assays. The results showed that the pCsVMV was able to drive high gene expression of β–glucuronidase reporter gene (UidA) in the transient assays in cassava somatic embryo. Expression of the gene also increases with the increase in the day of cocultivation and likewise expression of the gene was higher for the sample in the light than the dark.
Studies on amyloid formation in familial amyloidotic polyneuropathy

v Part I Introduction General Introduction 1 1. Amyloid 1 1.1. Biochemical features of amyloid 1 2. Amyloid diseases 2 2.1. Localized amyloidosis 4 2.1.1. Polypeptide hormone derived (PHD) amyloids 4 2.1. 2. A£ 4 2.1. 3. Atub 6 2.1. 4. APrP 6 2.2. Systemic amyloidosis 6 2.2.1. ACys 6 2.2.2. AA amyloidosis 7 2.2.3. Aapo AI 7 2.2. 4. Aapo All 7 2.2. 5. A02M 7 2.2. 6. AFib A 8 2.2. 7. AL, AH 8 2.2. 8. Agel 8 2.2. 9. ALys 9 2.3. ATTR amyloidosis 9 2.3.1. Familial amyloidotic polyneuropathy 9 2.3. 2. Familial amyloidotic cardiomyopathy 10 2.3. 3. Others 12 2.3. 4. Non amyloidogenic variants and compound hétérozygotes 12 2.3. 5. Senile systemic amyloidosis 13 2.3. 6. Biochemical features of transthyretin 14 3. Models of amyloidogenesis 18 3.1. Amyloidogenic potential 19 3.1.1 ATTR 19 3.1. 2. AA 21 3.1. 3. AL 22 3.1. 4. Polypeptide hormone derived amyloid 22 3.1. 5. A£ 23
High Accuracy and Short Delay 1ch-SSVEP Quadcopter-BMI Using Deep Learning

This study considers a brain-machine interface (BMI) system based on the steady state visually evoked potential (SSVEP) for controlling quadcopters using electroencephalography (EEG) signals. An EEG channel with a single dry electrode, i.e., without conductive gel or paste, was utilized to minimize the load on users. Convolutional neural network (CNN) and long short-term memory (LSTM) models, both of which have received significant research attention, were used to classify the EEG data obtained for flickers from multi-flicker screens at five different frequencies, with each flicker corresponding to a drone movement, viz., takeoff, forward and sideways movements, and landing. The subjects of the experiment were seven healthy men. Results indicate a high accuracy of 97% with the LSTM model for a 2 s segment used as the unit of processing. High accuracy of 93% for 0.5 s segment as a unit of processing can remain in the LSTM classification, consequently decreasing the delay of the system that may be required for safety reasons in real-time applications. A system demonstration was undertaken with 2 out of 7 subjects controlling the quadcopter and monitoring movements such as takeoff, forward motion, and landing, which showed a success rate of 90% on average.
Effect of seed priming with molybdenum on performance of rainfed chickpea (Cicer arietinum L.)

A field experiment was conducted during the Rabi seasons in 2009–10 and 2010–11 at Punjab Agricultural University Regional Research Station for Kandi Area, Ballowal Saunkhri to study the effect of seed priming with molybdenum (Mo) on chickpea (Cicer arietinum L.) variety PBG 1. Four treatments comprising seed priming with 250, 500 and 750 ppm solution of molybdenum and untreated control were laid out in randomized complete block design with four replications. Plant height, number of pods/plant, test weight, seed yield, straw yield and rain water use efficiency increased with increasing levels of Mo seed priming upto 500 ppm. Dry weight of root nodules increased upto 750 ppm of Mo. All the levels of Mo were significantly superior to untreated control for most of the characters. Seed priming with 500 ppm of Mo resulted into 18.9% higher seed yield over control. Higher net returns and B:C ratio were also observed in case of 500 ppm Mo treatment. The study suggested that productivity and returns from rainfed chickpea can be improved through a simple low-cost seed priming (with 500 ppm Mo) technology.
Matching Pursuit Shrinkage in Hilbert Space

—This paper contains the study on a hybrid algorithm combining Matching Pursuit (MP) and wavelet shrinkage. In this algorithm, we propose to shrink the scalar product of the element that best correlates with the residue, before modifying the residue. The study concerns for a rather broad family of shrinkage functions. Using simple properties of these shrinkage functions, we show that the algorithm converges towards the orthogonal projection of the data on the linear space generated by the dictionary, modulo a precision characterized by the shrinkage function. Finally, under a mild assumption on the shrinkage function (for instance, the hard shrinkage satisﬁes this assumption), this algorithm converges in a ﬁnite time which can be estimated from the properties of the shrinkage function. Experimental results demonstrate that in the presence of noise, our new algorithm outperforms the original MP algorithm when the the correlation of dictionary with the noise is not negligible.
Seasonal hydrology shifts production sources supporting fishes in rivers of the Lower Mekong Basin

Seasonal hydrology is assumed to be an important reason why the Lower Mekong Basin supports highly productive and biodiverse inland fisheries. We used C and N stable isotope ratios of tissue samples to estimate primary production sources supporting fish biomass in the Mekong and three large tributaries in Cambodia. We used a Bayesian mixing model to estimate relative contributions of four alternative production sources — seston, benthic algae, riparian grasses, and riparian macrophytes. There was little seasonal variation in isotopic signatures of riparian plants, but benthic algae and seston showed large seasonal shifts in carbon ratios. Seston and benthic algae were the most important production sources supporting fish biomass overall during the dry season, and riparian vegetation was the most important source during the wet season. Sources contributed differentially to biomass of trophic and habitat guilds, especially during the dry season. A dam on the upper Sesan River has changed hydrology, channel .
Improved streaming quotient filter: a duplicate detection approach for data streams

The unprecedented development and popularization of the Internet, combined with the emergence of a variety of modern applications, such as search engines, online transactions, climate warning systems and so on, enables the worldwide storage of data to grow unprecedented. Efficient storage, management and processing of such huge amounts of data has become an important academic research topic. The detection and removal of duplicate and redundant data from such multi-trillion data, while ensuring resource and computational efficiency, has constituted a challenging area of research.Because of the fact that all the data of potentially unbounded data streams can not be stored, and the need to delete duplicated data as accurately as possible, intelligent approximate duplicate data detection algorithms are urgently required. Many well-known methods based on the bitmap structure, Bloom Filter and its variants are listed in the literature. In this paper, we propose a new data structure, Improved Streaming Quotient Filter (ISQF), to efficiently detect and remove duplicate data in a data stream. ISQF intelligently stores the signatures of elements in a data stream, while using an eviction strategy to provide near zero error rates. We show that ISQF achieves near optimal performance with fairly low memory requirements, making it an ideal and efficient method for repeated data detection. It has a very low error rate. Empirically, we compared ISQF with some existing methods (especially Steaming Quotient Filter (SQF)). The results show that our proposed method outperforms theexisting methods in terms of memory usage and accuracy.We also discuss the parallel implementation of ISQF
Statistical issues on the design and analysis of cancer immunotherapy trials

The recent introduction of cancer immunotherapies has heralded an era of significant change in the treatment of cancers. The indirect mechanisms of action of cancer immunotherapies stimulate the patient's own immune system to fight against cancers by targeting antigens expressed on cancer cells and kick starts the antitumor effects. Monoclonal antibodies (mAbs) represent a significant subset of immunotherapy agents that are currently being used to treat cancers. Examples of such agents include ipilimumab, a fully human IgG1 that blocks cytotoxic T lymphocyte-associated protein 4 (CTLA-4), or nivolumab, a fully human IgG4 that selectively blocks the interaction of the PD-1 receptor with its two known programmed death ligands, PD-L1 and PD-L2 (1). ThesemAbs have shown striking antitumor activities in patients with melanoma or other cancers. The efficacy and safety profiles differ from those of previously characterized cytotoxic and pathway-specific agents. Some of the unique characteristics displayed by the cancer immunotherapies, e.g., immune checkpoint inhibitors, include the promising long-term survival and delayed clinical effects. In addition, the endpoints and the conventional approach of assessing antitumor activity derived from chemotherapeutic agents may not adequately capture extended clinical benefit from immunotherapies. Consistent with the idea that immunotherapies fight cancers by augmenting the immune response, most adverse events are expected to be inflammatory in nature. The introduction of these new therapies warrants a closer look at the endpoints as well as the conventional assessment approaches in efficacy and safety.
EVOLUTION OF THE HUMAN RHO GTPASE FAMILY Conservation And Diversity

The Rho GTPases form a relatively old family of signalling proteins, with representation across all branches of the eukaryote lineage. As a consequence of this, there is a large amount of sequence information relating to Rho GTPases in the rapidly increasing number of genome and cDNA databases. This kind of data is never a substitute for 'wet' experimental work in terms of understanding protein function; however, it can tell us something about the history of the proteins we work with. By understanding the history of these signalling proteins, we can more accurately draw together the growing body of experimental work on Rho GTPase function in various genetic model organisms. In this short review we look at the origins of the human Rho GTPase family and attempt to trace the emergence of specific isoforms. We also examine two other factors that contribute to the overall diversity of human Rho GTPase proteins: genetic polymorphism and alternative splicing.
ACCIONES LIPOSTÁTICAS DE LA LEPTINA ACTUANDO VÍA SISTEMA NERVIOSO CENTRAL: MECANISMOS MOLECULARES EN EL HÍGADO Y EN EL TEJIDO ADIPOSO

RESUMEN DE LA TESIS La leptina actuando via central o periferica disminuye la ingesta, la adiposidad y aumenta la sensibilidad a insulina del organismo como un todo. La dilucidacion de las vias de senalizacion de la leptina y de los mecanismos que provocan la resistencia a la misma, son factores claves para entender el fenomeno de la obesidad y la Diabetes tipo II, asi como para permitir el desarrollo de una manera consciente de farmacos que corrijan estas patologias. En la presente tesis se abordan algunos mecanismos moleculares responsables de los efectos lipostaticos y sensibilizantes a insulina de la leptina actuando a traves del sistema nervioso central. Especificamente, se ha estudiado el efecto de la leptina suministrada por via central sobre el metabolismo lipidico en higado y tejido adiposo epididimal (TAE). Asimismo, en el TAE se analizo la influencia de la leptina central sobre el metabolismo de los esfingolipidos y sobre la cascada de senalizacion de insulina. Finalmente, en animales envejecidos, que constituyen un modelo con resistencia central a la leptina, se analizaron las alteraciones en el metabolismo lipidico en el higado y el TAE, y del metabolismo del los esfingolipidos en el TAE. Como resultado, se obtuvo que la leptina actuando solamente sobre el sistema nervioso central y de forma independiente de sus propiedades anorexigenas, provoca adaptaciones metabolicas especificas de tejido en el higado y el TAE, que limitan la acumulacion de TAG y AG libres en ambos tejidos y reducen el contenido de TAG en el plasma. Asi, la leptina central promueve un incremento de la b-oxidacion de los AG, y a su vez, un aumento de la lipolisis en el TAE. Los AG liberados son capturados y oxidados fundamentalmente por el higado, donde via PPARa y PGC-1a, se incrementa la expresion de enzimas involucradas en la captura y b-oxidacion de AG. Adicionalmente, en el higado la leptina disminuye la lipogenesis a traves de la inhibicio