Locating regions in a sequence under density constraints

Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence matching. Mathematically, this corresponds to searching a string of 0s and 1s for a substring whose relative proportion of 1s lies between given lower and upper bounds. We consider the algorithmic problem of locating the longest such substring, as well as other related problems (such as finding the shortest substring or a maximal set of disjoint substrings). For locating the longest such substring, we develop an algorithm that runs in O(n) time, improving upon the previous best-known O(n log n) result. For the related problems we develop O(n log log n) algorithms, again improving upon the best-known O(n log n) results. Practical testing verifies that our new algorithms enjoy significantly smaller time and memory footprints, and can process sequences that are orders of magnitude longer as a result.Comment: 17 pages, 8 figures; v2: minor revisions, additional explanations; to appear in SIAM Journal on Computin

Linking occurrence and changes in local abundance of farmland bird species to landscape composition and land-use changes

Changes in agricultural policies have caused dramatic changes in land-use in agricultural landscapes. To investigate whether such changes in land-use relate to temporal changes in bird communities a repeated inventory (1994 and 2004) of farmland birds was made in 212 point-count sites in south-central Sweden.Distinct changes in abundance of several species over the study period were recorded, abundance of the 16 studied species decreased by 23%. The decline was significant for eight species, while two species increased significantly. Persistence and colonisation models suggested similar species-habitat relationships as the snapshot models, i.e. eight of the 12 associations were in line with what could be expected from the snapshot models. Occurrence of nine species was linked to land-use whereas six species displayed links between changes in occurrence and changes in land-use. In line with previous studies positive effects of short rotation coppice and negative effects of autumn-sown crops were found, while set-asides showed fewer effects than expected. In the snapshot models several species showed links to landscape characteristics such as amount of forest (negative for five species) and landscape heterogeneity (positive for six species). The evidence for effects of the landscape variables on persistence/colonisation was more restricted.The results suggest that both land-use changes and the landscape setting may cause local changes in abundance of farmland birds, even for species displaying a general decline in numbers between years, the effects of land-use changes being, however, strongly species specific. (C) 2014 Elsevier B.V. All rights reserved

Analisis Perbandingan Performansi Dan Pemilihan Web Browser (Studi Kasus: Universitas Siliwangi)

Semakin berkembangnya browser baik dari segi performansi maupun jumlah yang kerap membuat pengguna bingung untuk memilih dan tidak memanfaatkan fitur yang ditawarkan browser secara penuh. Dengan melakukan analisis perbandingan dan pembuatan panduan pemilihan browser, pengguna browser diharapkan dapat memilih browser secara lebih objektif dan sesuai dengan kebutuhan. Metodologi yang digunakan dalam penelitian ini adalah survey analitik dengan pendekatan cross sectional. Analisis performansi dilakukan dengan browser yang berbeda, yang dipilih berdasarkan tingkat popularitas, layout engine, speciality dan versi terbaru dari masing – masing browser tersebut. Faktor penilaian browser adalah dukungan terhadap standar web, kecepatan menampilkan HTML, kecepatan memproses ECMAScript, tingkat keamanan browser, konsumsi hardware dan fitur browser. Setelah pengujian performansi browser, dilakukan survey terhadap pengguna untuk mendapatkan data yang dianalisis untuk mempelajari tren – tren penggunaan browser. Dengan menggunakan hasil analisis performansi browser dan tren pengguna, dibangun rekomendasi pemilihan browser berdasarkan kebutuhan individu pengguna serta panduan pemilihan browser yang direkomndasikan. Sedangkan pengujian hipotesis dilakukan untuk mengetahui tingkat hubungan dan pengaruh antara tren penggunaan browser terhadap performansi browser. Analisis performansi serta rekomendasi dan panduan yang telah dibangun sebaiknya terus dikembangkan dan diperbaharui seiring dengan munculnya browser generasi baru

Experimental and modeling study of heterogeneous ice nucleation on mineral aerosol particles and its impact on a convective cloud

Eine der größten Herausforderungen zur Vorhersage des Klimawandels liegt im Verständnis der Rolle von Eisnukleation auf die Entwicklung troposphärischer Wolken. Mit einer neuentwickelten feuchtigkeitskontrollierten „Cold Stage“wurden bis zu 200 monodispe Tröpfchen, bestehend aus einer K-feldspar Suspension, beobachtet. Die Eisnukleationsfähigkeiten von individuellen Residualpartikeln für Immersionsgefrieren und Depositionnukleation und ihre Wechselwirkung wurden untersucht. Die ersten Ergebnissen zeigten, dass die gleichen eisaktiven Stellen am Immersiongefrieren und an der Depositionnukleation beteiligt sind. Die atmospährischen Auswirkungen unserer experimentellen Ergebnisse wurden mit Descam (Flossmann et al., 1985), einem 1.5d detaillierte Mikrophysikmodell, untersucht in einer Fallstudie zur Rolle verschiedener Eisnukleationsmechanismen auf die dynamische Entwicklung der CCOPE konvektive Wolke (Dye et al., 1986). Vier Mineralaerosoltypen (K-Feldspath, Kaolinit, Illit und Quartz) trugen zum Immersion- und Kontaktgefrieren und zur Depositionnukleation bei durch explizite Ice Nukleation Aktive Stellen Dichte Parametrisierungen. Die verschiedenen Aerosoltypen und Eisnukleationsmechanismen wurden in Empfindlichkeitsstudien getrennt und zusammen behandelt, um ihre relative Bedeutung zu beurteilen. Immersiongefrieren auf K-Feldspath Partikeln zeigte die größte Wirkung auf eine konvektiven Wolke

DTB 078 Hiron Stiell Spencer 6-4-2023

In this interview, Hiron Stiell Spencer is interviewed by Kern Jackson and Rachel Hines at Prince of Peace Church about her memories of growing up in the Down the Bay community, the meaning of the community to her today, and the relationship between Down the Bay and the congregation at Prince of Peace. Ms. Spencer also describes businesses that she remembers from growing up in the neighborhood, some biographical details, and some of her family history

Effects of deletion of the Streptococcus pneumoniae lipoprotein diacylglyceryl transferase gene lgt on ABC transporter function and on growth in vivo

Lipoproteins are an important class of surface associated proteins that have diverse roles and frequently are involved in the virulence of bacterial pathogens. As prolipoproteins are attached to the cell membrane by a single enzyme, prolipoprotein diacylglyceryl transferase (Lgt), deletion of the corresponding gene potentially allows the characterisation of the overall importance of lipoproteins for specific bacterial functions. We have used a Δlgt mutant strain of Streptococcus pneumoniae to investigate the effects of loss of lipoprotein attachment on cation acquisition, growth in media containing specific carbon sources, and virulence in different infection models. Immunoblots of triton X-114 extracts, flow cytometry and immuno-fluorescence microscopy confirmed the Δlgt mutant had markedly reduced lipoprotein expression on the cell surface. The Δlgt mutant had reduced growth in cation depleted medium, increased sensitivity to oxidative stress, reduced zinc uptake, and reduced intracellular levels of several cations. Doubling time of the Δlgt mutant was also increased slightly when grown in medium with glucose, raffinose and maltotriose as sole carbon sources. These multiple defects in cation and sugar ABC transporter function for the Δlgt mutant were associated with only slightly delayed growth in complete medium. However the Δlgt mutant had significantly reduced growth in blood or bronchoalveolar lavage fluid and a marked impairment in virulence in mouse models of nasopharyngeal colonisation, sepsis and pneumonia. These data suggest that for S. pneumoniae loss of surface localisation of lipoproteins has widespread effects on ABC transporter functions that collectively prevent the Δlgt mutant from establishing invasive infection

Studi Analisis Rugi-rugi Baterai Tipe Alumunium Udara pada Beban Listrik Statis

Rugi-rugi baterai tipe alumunium udara (Al-udara) pada beban listrik statis telah dianalisis. Sel baterai Al udara berbentuk segi empat dengan panjang 6 cm, lebar 5 cm, dan tebal 1 cm. Baterai menggunakan plat Al, KOH, tissue, dan silika xerogel berturut-turut sebagai anoda, elektrolit, separator dan bahan aktif katoda udara. Karakteristik baterai ditentukan dengan memvariasikan lamanya charging dan pengisian ulang larutan elektrolit ke dalam sel baterai. Sel baterai dikarakterisasi menggunakan metode Electrochemical Impedance Spectroscopy (EIS) dan Battery Testing System (BTS). Modul baterai dikonfigurasi dengan 12 sel baterai yang tersusun secara paralel/seri. Modul baterai diuji ke beban listrik statis menggunakan lampu Light Emitting Diode (LED) berdaya 75 mW. Rugi-rugi baterai Al-udara (impedansi karakteristik) sebelum dan setelah pengosongan pada lampu LED dibandingkan dan dianalisis. Hasil menunjukkan bahwa arus pengosongan optimum baterai adalah 0.8 mA dan kapasitas maksimum 0,59 mAh. Pada pengujian beban LED, pengulangan charging baterai menurunkan waktu uji dan suplai daya baterai terhadap beban. Waktu uji baterai dan daya suplai baterai terhadap beban LED berturut-turut menurun dari 185 menit menjadi 7 menit dan dari 18,69 mWatt menjadi 3,14 mWatt jika baterai melakukan pengulangan charging dari charging pertama sampai charging keempat, sehingga rugi-rugi daya sekitar 83,19% dari daya originalnya untuk sampai ke pengulangan charging keempat

KRAS-mutation status dependent effect of zoledronic acid in human non-small cell cancer preclinical models

BACKGROUND: In non-small cell lung cancer (NSCLC) KRAS-mutant status is a negative prognostic and predictive factor. Nitrogen-containing bisphosphonates inhibit prenylation of small G-proteins (e.g. Ras, Rac, Rho) and thus may affect proliferation and migration. In our preclinical work, we investigated the effect of an aminobisphosphonate compound (zoledronic acid) on mutant and wild type KRAS-expressing human NSCLC cell lines. RESULTS: We confirmed that zoledronic acid was unable to inhibit the prenylation of mutant K-Ras unlike in the case of wild type K-Ras. In case of in vitro proliferation, the KRAS-mutant human NSCLC cell lines showed resistance to zoledronic acid wild-type KRAS-cells proved to be sensitive. Combinatory application of zoledronic acid enhanced the cytostatic effect of cisplatin. Zoledronic acid did not induce significant apoptosis. In xenograft model, zoledronic acid significantly reduced the weight of wild type KRAS-EGFR-expressing xenograft tumor by decreasing the proliferative capacity. Futhermore, zoledronic acid induced VEGF expression and improved in vivo tumor vascularization. MATERIALS AND METHODS: Membrane association of K-Ras was examined by Western-blot. In vitro cell viability, apoptotic cell death and migration were measured in NSCLC lines with different molecular background. The in vivo effect of zoledronic acid was investigated in a SCID mouse subcutaneous xenograft model. CONCLUSIONS: The in vitro and in vivo inhibitory effect of zoledronic acid was based on the blockade of cell cycle in wild type KRAS-expressing human NSCLC cells. The zoledronic acid induced vascularization supported in vivo cytostatic effect. Our preclinical investigation suggests that patients with wild type KRAS-expressing NSCLC could potentially benefit from aminobisphosphonate therapy

Air Quality Monitoring in Briquette Industrial Environments through Air Particle Detection Systems

Air is the most basic need for the survival of living things, especially humans. Briquetting plants are one of the industries that produce airborne particles harmful to human health and the surrounding environment. These particles can cause respiratory problems and serious illnesses if not properly detected and controlled. Therefore, an air particle detection system is indispensable for monitoring air quality in the factory environment. PT Arkelindo Bara Sejahtera, as a company engaged in the manufacture of briquettes, has a negative impact on the environment, especially air pollution due to the carbonization process that produces smoke and dust. The implementation of this community service activity aims to improve air quality in the briquette industry environment through the implementation of an air particle detection system. This activity includes socialization about the dangers of air particles, training on the use of detection devices, and filling out questionnaires to evaluate participants' understanding. The results of this activity show that the air quality in the factory environment is still poor with high Air Quality Index (AQI) values, mainly caused by the carbonization process. However, this activity succeeded in raising the awareness of the factory staff on the importance of air quality monitoring and providing concrete recommendations to reduce particle emissions, including the use of cleaner fuels and improving the efficiency of the carbonization process. Thus, it is hoped that this activity can help prevent more severe air pollution in the future and protect the health of the surrounding community