Enhanced maps of transcription factor binding sites improve regulatory networks learned from accessible chromatin data

Determining where transcription factors (TFs) bind in genomes provides insight into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances in high-throughput profiling of regulatory DNA have yielded large amounts of information about chromatin accessibility. Interpreting the functional significance of these data sets requires knowledge of which regulators are likely to bind these regions. This can be achieved by using information about TF-binding preferences, or motifs, to identify TF-binding events that are likely to be functional. Although different approaches exist to map motifs to DNA sequences, a systematic evaluation of these tools in plants is missing. Here, we compare four motif-mapping tools widely used in the Arabidopsis (Arabidopsis thaliana) research community and evaluate their performance using chromatin immunoprecipitation data sets for 40 TFs. Downstream gene regulatory network (GRN) reconstruction was found to be sensitive to the motif mapper used. We further show that the low recall of Find Individual Motif Occurrences, one of the most frequently used motif-mapping tools, can be overcome by using an Ensemble approach, which combines results from different mapping tools. Several examples are provided demonstrating how the Ensemble approach extends our view on transcriptional control for TFs active in different biological processes. Finally, a protocol is presented to effectively derive more complete cell type-specific GRNs through the integrative analysis of open chromatin regions, known binding site information, and expression data sets. This approach will pave the way to increase our understanding of GRNs in different cellular conditions

FREEZE-THAW DURABILITY OF PORTLAND CEMENT CONCRETE DUE TO ADDITION OF CRUMB RUBBER AGGREGATES

Ground tire rubber also known as crumb rubber has been widely used in asphalt concrete over the past several years due to its ability to improve temperature susceptibility of asphalt binders and enhance the performance of asphalt pavements. However, its inclusion in portland cement concrete is comparatively recent and more research is needed before adopting it as a regular construction material. Past research has shown that while addition of rubber aggregates in concrete reduces its compressive, tensile and flexural strengths, but is useful in improving durability properties as freeze-thaw resistance due to the ability of crumb rubber to generate an effective air-void system in rubberized concrete. Previous studies have focused on the effect of the addition of the various sizes and replacement levels of crumb rubber on strength and other mechanical properties; however, a comprehensive assessment of these variables on freeze-thaw durability or air void parameters due to the ambient and cryogenic types of crumb rubber has not yet been fully conducted. The results of such investigations would potentially address issues such as instability and the loss of air and its effect on the air-void system in conventionally air-entrained concretes. To address this need, the main objective of this study was to investigate the freeze-thaw durability of rubberized portland cement concrete through the addition of two types of crumb rubber particles, ambient and cryogenic. In addition, three sizes of crumb rubber aggregates, #8 (2.36 mm), #50 (0.60 mm) and #100 (0.30 mm) at three replacement levels, 8%, 16% and 24%, by volume of fine aggregates were used in the preparation of the concrete specimens. The results of rubberized concrete were compared with both non-air-entrained concrete and air-entrained concrete without the addition of rubber. The effect of the alkalinity of cement, the absence of super-plasticizer, the vibration time and frequency of the consolidation of fresh concrete, and the addition of supplementary cementing materials with high loss-on-ignition (LOI) that affects the air content in concrete, such as rice husk ash, was studied. Also, comparative studies were conducted with latex emulsions to understand if crumb rubber has any similarity with latex on concrete properties. The investigations on freeze-thaw durability of crumb rubber concrete concluded that the use of finer sized particles i.e. #50 and #100 of both types of crumb rubber at 16% and 24% replacement levels, by volume of sand, displayed improved durability performance in freeze-thaw test without the need for conventional air-entraining admixtures. Concrete mixtures containing finer crumb rubber for higher dosage levels in combination with both low-alkali and high-alkali cements exhibited higher durability factors, of more than 60% at the end of 300 F-T cycles, as compared to the non-air entrained control concrete and coarser rubber concrete specimens. It was observed that the system of air bubbles incorporated in concrete due to the addition of crumb rubber particles was not adversely affected by the high carbon content in the #50 size ambient crumb rubber concrete specimens with rice husk ash (RHA), the different vibration frequency for consolidation of ambient crumb rubber concrete and in the absence of super-plasticizer in combination with the low alkali cement. Also, the vibration time in cryogenic rubber concrete did not affect its F-T performance. The F-T performance of latex modified concrete with the low alkali cement was also comparable to the finer size crumb rubber concrete. However, the rubber concrete specimens prepared from combinations of RHA with #100 size and both low and high alkali cement along with #50 size crumb rubber concrete specimens with high alkali cement negatively affected the F-T performance. The vibration time in ambient rubberized concrete specimens affected their performance indicating that these factors affect the air entrainment in rubberized concrete similar to the conventionally air entrained concrete mixtures. Also, the latex modified concrete with higher replacement levels and high alkali cement was not effective in providing adequate F-T performance as compared to the crumb concrete with finer size and higher replacement levels. In summary, the findings from this research indicate that the use of finer rubber sizes and higher rubber replacement levels, improves the freeze-thaw durability performance of concrete, even though the strength of the concrete is decreased. However, a difference in the properties of rubberized concrete with #50 and #100 size fractions was observed in the various parameters studied here which needs to be investigated in further depth. The use of rubberized concrete is recommended in applications where the strength requirements are minimal but high durability requirements need to be satisfied. The hydrophobic nature of the crumb rubber and increased specific surface area (SSA) of finer size fractions of crumb rubber particles appears to be the principal mechanism leading to the increased air entrainment in the rubberized concrete. Standard petrographic examination methods are adequate to characterize the air content parameters even in rubberized concretes. If the finer crumb rubber particles can be used as a partial replacement to fine aggregates, it can reduce the usage of natural mineral aggregates greatly and minimize their rapid depletion. Crumb rubber particles may prove to be a sustainable option for producing frost resistant concrete and also provide an opportunity for economic and environmental friendly solution for the disposal of high amount of waste tires in the landfills

Activating Background Knowledge: An Effective Strategy to Develop Reading Comprehension Skills

The present paper is a report on a small classroom based research study. The researcher has tried Activating Background Knowledge as a strategy to improve reading comprehension skills of the students in the First Year B.Com. Classroom in a degree college affiliated to the University of Mumbai. The teacher-researcher assigned two passages dealing with two different social issues and set in two different contexts, i.e., foreign and local, for comprehension to the students in the classroom. The classroom experience indicated that activating and building on the students’ background knowledge did help in facilitating their reading comprehension skills. The paper thus recommends it as an effective strategy to develop the students’ reading comprehension skills

TF2Network : predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information

A gene regulatory network (GRN) is a collection of regulatory interactions between transcription factors (TFs) and their target genes. GRNs control different biological processes and have been instrumental to understand the organization and complexity of gene regulation. Although various experimental methods have been used to map GRNs in Arabidop-sis thaliana, their limited throughput combined with the large number of TFs makes that for many genes our knowledge about regulating TFs is incomplete. We introduce TF2Network, a tool that exploits the vast amount of TF binding site information and enables the delineation of GRNs by detecting potential regulators for a set of co-expressed or functionally related genes. Validation using two experimental benchmarks reveals that TF2Network predicts the correct regulator in 75-92% of the test sets. Furthermore, our tool is robust to noise in the input gene sets, has a low false discovery rate, and shows a better performance to recover correct regulators compared to other plant tools. TF2Network is accessible through a web interface where GRNs are interactively visualized and annotated with various types of experimental functional information. TF2Network was used to perform systematic functional and regulatory gene annotations, identifying new TFs involved in circadian rhythm and stress response

Analysis of physics research output of SP Pune University during the period 1990-2014

The paper analyzes the research contributions by the faculty members of the Department of Physics, Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India for the period 1990-2014. Bibliographic and citation data were retrieved from Scopus database. Query statements covering all variations in the name of SPPU were used to search the database. Scopus indexed 1629 publications with 22618 citations for the period. Author keywords in Scopus database indicate that faculty members are working in core areas of physics as well as interdisciplinary subjects like chemistry, instrumentation sciences, engineering, etc. The year-wise analysis shows that research productivity of faculty member increased over the period. Faculty members published their research in core physics journals among which Journal of Applied Physics (72 papers) is the most preferred journal. The faculty members of the University have collaborated with scientists from USA, UK, Germany and Japan. At the national level, the University physicists have collaborated most with Bhabha Atomic Research Centre

The correlation of visual inspection, Pap-smear and immunocytochemistry of human papilloma virus in detection of cervical cytology

Background: Carcinogenicity presents as a major challenge to scientists and society.. Cervical cancer ranks fifth in the world and is the second cause of death in developing countries like India and China. The rate of death due to cervical cancer is greatest in India. At any time women are at risk of harboring HPV infection, which has been seen to cause cervical cancer. Clinical judgment should be used in spite of all high quality modalities available for screening and diagnosis, as initiated by WHO (World health organization) the Down Staging of cervical cancer, VIA, VILI, Pap smear introduced by George Papanicolaou in 1940s , HPV testing by Immunocytochemistry (ICC) and  HPV DNA , Colposcopy , are other modalities to screen cervix. The study aims to evaluate the correlation between Pap smear, visual inspection and Immunocytochemistry of Human papilloma virus (HPV).Methods: All 100 consecutive women were subjected to visual inspection of cervix, Pap smear and immunocytochemistry of HPV. Pap smear was done by conventional method.Results: it was seen that out 100 consecutive cervico-vaginal, ears for Pap and Immunocytochemistry, only 33 were abnormal, 24 were ASCUS, 6 were LSIL, 2 were HSIL, 1 was SCC and 67 were NILM out of which 3 were reactive for ICC. And all 33 were reactive for ICC.Conclusions: The p16 immunostaining performed on conventional smears can become alternative or addition to l HPV DNA tests. The Bethesda System (TBS) 2001 for reporting cervical cytology diagnosis is of high value in detecting abnormal cervical cytology. It is further concluded that the ancillary screening for HPV in NILM category seems to be not advisable as percentage of detection of HPV in this category is low. 

Effect of L-arginine on amniotic fluid index in oligohydramnios

Background: Oligohydramnios is a common diagnosis in obstetrics and carries an increased risk of operative interference and perinatal mortality and morbidity. Identification and proper management of oligohydramnios can result in a favourable outcome. The administration of L-arginine (nitric oxide donor) has been suggested to improve the amniotic fluid index (AFI) in oligohydramnios.Methods: This is a prospective study conducted over a period of two years. A total of 100 women attending antenatal clinic of Acharya Vinoba Bhave Rural Hospital, Sawangi (Meghe), Wardha who were diagnosed with oligohydramnios were included. Women who fulfilled the inclusion criteria were prescribed sachets of L-arginine containing 3g of the active ingredient for periods varying between 1 to 4 weeks. Change in AFI was noted.Results: L-arginine increases the amniotic fluid index in cases of oligohydramnios by 2.03±0.39 cm.Conclusions: L-arginine could be a potent treatment option for treatment of oligohydramnios. However extensive long-term studies are required to demonstrate not only its efficacy but also effect on maternal and perinatal outcome

Epidemiological study of clinical characteristics of patients with PCOS attending infertility clinic and awareness of PCOS in a rural set up

Background: Polycystic ovarian syndrome (PCOS) is one of the most common endocrine disorders in women of reproductive age group.It is a common diagnosis in women presenting with infertility.All the dimensions of PCOS have not been completely explored.In this study we studied the clinical features of PCOS and comparing with non-PCOS infertility patients and simultaneously studied the prevalence of PCOS in infertility patients and its awarenessin a rural set up.Methods:It is a prospective observational study carried out over a period of 15 months at infertility clinic Acharya Vinoba Bhave Rural Hospital in Maharashtra,India in 100 infertility patients.Results:54 out of 100 infertility patients had PCOS.16 out of 54 had oligomenorrhoea in contrast to 10 out of 46 in non PCOS.38 PCOS patients had multiple follicles which only 18 non PCOS had.There was a significant difference in androgenic features of PCOS and non PCOS but not in BMI and WHR. Only 10 patients were aware regarding PCOS.Conclusion:PCOS is one of the important factors causing infertility.It is an ill defined symptom complex needing its due attention.There is a need to increase awareness regarding.The clinical featuresof PCOS are heterogeneous and thus can be investigated accordingly of selection of appropriate treatment modality