Alignment of helical membrane protein sequences using AlignMe

Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments. Existing approaches typically consider membrane-related information either by using membrane-specific substitution matrices or by assigning distinct penalties for gap creation in transmembrane and non-transmembrane regions. Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments. We tested various strategies using a specifically designed program called AlignMe. An updated set of homologous membrane protein structures, called HOMEP2, was used as a reference for optimizing the gap penalties. The best of the membrane-protein optimized approaches were then tested on an independent reference set of membrane protein sequence alignments from the BAliBASE collection. When secondary structure (S) matching was combined with evolutionary information (using a position-specific substitution matrix (P)), in an approach we called AlignMePS, the resultant pairwise alignments were typically among the most accurate over a broad range of sequence similarities when compared to available methods. Matching transmembrane predictions (T), in addition to evolutionary information, and secondary-structure predictions, in an approach called AlignMePST, generally reduces the accuracy of the alignments of closely-related proteins in the BAliBASE set relative to AlignMePS, but may be useful in cases of extremely distantly related proteins for which sequence information is less informative. The open source AlignMe code is available at https://sourceforge.net/projects/alignme​/, and at http://www.forrestlab.org, along with an online server and the HOMEP2 data set

Studi Deskriptif Tingkat Pengetahuan Ibu Tentang Ascariasis (Cacingan) pada Balita di Wilayah Kerja Puskesmas Siwuluh Kabupaten Brebes Tahun 2019

Cacingan merupakan kondisi di dalam tubuh manusia terdapat cacing. Cacingan dapat mengakibatkan menurunnya kondisi kesehatan, gizi, kecerdasan, dan produktivitas penderitanya sehingga secara ekonomi banyak menyebabkan kerugian. Cacingan bisa terjadi pada orang dewasa namun lebih banyak kejadian terjadi pada usia anak-anak. Hal ini dapat disebabkan anak yang kurang menjaga kebersihan diri terutama pada saat mereka sedang bermain. Penelitian ini bertujuan untuk mengetahui pengetahuan ibu tentang gambaran tingkat pengetahuan ibu tentang ascariasis (cacingan) pada Balita di Wilayah Kerja Puskesmas Siwuluh Kabupaten Brebes. Metode penelitian yang digunakan adalah deskriptif dengan metode survey yang bertujuan untuk mengetahui gambaran pengetahuan ibu tentang cacingan pada Balita di Wilayah Puskesmas Siwuluh. Pengambilan data menggunakan kuesioner. Berdasarkan hasil penelitian 50 responden ibu yang mempunyai Balita, menunjukkan pengetahuan responden dikategorikan berpengetahuan baik sebanyak 9 responden (18%), Cukup sebanyak 13 responden (26%), dan kurang 28 responden (56%). Dapat disimpulkan bahwa sebagian besar ibu di Wilayah Kerja Puskesmas Siwuluh berpengetahuan kurang. Hasil penelitian ini dapat dijadikan acuan untuk data awa

OPTIMALISASI CORPORATE SOSIAL RESPONSIBILITY BUMN UNTUK KAWASAN SUNGAI CIKAPUNDUNG BANDUNG

Today the application of CSR becomes increasingly important for the company. CSR has become a necessity for companies. The company's presence in the midst of society's dependence coined by people who are nearby. The relationship between the company and the community share the two sides of a coin that can not be separated. CSR also contributed positively to the relationship between the company and the community. Company as part of the community has a role in the community. Companies are not only economic benefits hunt alone, but also a concern for the environment and social welfare. State-Owned Enterprises (SOEs) have a strategic role and functions, as executor of public services, balancing large private forces, and helped small business development. SOE CSR role in the preservation of rivers such as helping the government to regenerate the river Cikapundung as a public space and also regarding the handling of flooding in the area around the River Cikapundung Bandung. To find the best solution in the structuring of public space in this Cikapundung riverbank, is very important to develop a policy of restoration of the river that can balance the interests of economic, social and environmental sustainability sustainable

Makna Kepribadian Ganda dalam Music Video Goblin Karya Sulli

Peneltian ini berjudul Makna Kepribadian Ganda Dalam Music Video Goblin Karya Sulli. Penelitian ini bertujuan untuk mengetahui makna denotasi, makna konotasi, makna mitos pada music video Goblin karya Sulli. Penelitian ini menggunakan metode penelitian kualitatif, dengan pendekatan penelitian studi analisis semiotika Roland Barthes. Subyek penelitian ini adalah sebuah music video yang beberapa bagian adegannya menjadi obyek analisis, proses pengumpulan data dilakukan dengan studi pustaka, wawancara, diskusi dengan teman sejawat yaitu dengan menanyakan dan mendiskusikan bagian music video yang yang berhubungan dengan semiotika music video Goblin karya Sulli. Hasil penelitian ini menunjukkan bahwa dari hasil analisis dapat disimpulkan Secara makna denotasi music video ini menggambarkan penderita gangguan kepribadian ganda dengan tiga kepribadian yang berbeda. Secara makna konotasi music video ini menggambarkan bahwa dia selalu merasa kebingungan dan mempertanyakan identitas dia yang sebenarnya. Secara makna mitos music video ini menggambarkan bahwa memiliki kepribadian unik yang selalu berubah-ubah bukan karena ingin mendapatkan perhatian atau attention seeker.   Kata kunci: Semiotika, Makna, Kepribadian Ganda, Sulli, Roland Barthe

Evaluation of Machine Learning Models for Breast Cancer Diagnosis Via Histogram of Oriented Gradients Method and Histopathology Images

Breast cancer is the main death rate from malignant growth worldwide and the most frequently diagnosed type of cancer in females. Machine learning systems have been developed to assist in the accurate detection of cancer. There are numerous methods for cancer detection. But histopathological images are thought to be more precise. In this study, we used the HOG features extractor to extract statistical features from histopathology images of invasive ductal carcinoma. We chose the following images at random from the histopathology images: 100, 200, 400, 1000, and 2000. These statistical features were then used to train several algorithms, including the decision tree, quadratic discriminant analysis, extra randomized trees, gradient boosting, gaussian process classifier, naive bayes, nearest centroid, multilayer perceptron, and support vector machine, to identify whether or not the images depict cancerous or noncancerous growth. The algorithms' performance was evaluated depending on the specificity, accuracy, sensitivity, precision, F1_score, and AUC. The algorithms used worked best when the number of images was set to 100. As the number of images went up, their effectiveness went down

Sosialisasi Informasi Tanggap Bencana Daerah

Penelitian ini bertujuan untuk mengetahui bentuk, teknik dan proses sosialisasi informasi tanggap bencana daerah di Badan Penanggulangan Bencana Daerah (BPBD) Kabupaten Sukabumi. Penelitian ini menggunakan metode penelitian kualitatif dengan pendekatan studi deskriptif-kualitatif. Subjek penelitian adalah pegawai Badan Penanggulangan Bencana Daerah (BPBD) Kabupaten Sukabumi yang ditentukan secara purposive berdasarkan komunikasi publik. Proses pengumpulan data diperoleh melalui observasi objek dan wawancara mendalam, sedangkan untuk data penunjang diperoleh melalui studi dokumentasi, dan wawancara terhadap pihak yang terkait. Hasil penelitian ini menunjukan bahwa, menumbuhkan solidaritas antara masyarakat dengan Badan Penanggulangan Bencana Daerah (BPBD) sehingga tidak ada perbedaan (suku, agama, ras, dan golongan masyarakat), masyarakat menanggapi sangat baik penyuluhan yang dilakukan oleh Badan Penanggulangan Bencana Daerah (BPBD), dengan trauma healing memberikan tingkat keahlian yang baik kepada masyarakat, Badan Penanggulangan Bencana Daerah (BPBD) mengalami kendala anggaran dalam kegiatan sosialisasi, dan minimnya tenaga information technology (IT) untuk mengelola website BPBD Kabupaten Sukabumi.   Kata kunci: Komunikasi, Bentuk Sosialisasi, Tehnik Sosialisasi, Proses Sosialisas

Implementasi Kebijakan Penerimaan Peserta Didik Baru Sistem Zonasi Sekolah Menengah Pertama di Kecamatan Baleendah Kabupaten Bandung

Salah satu upaya untuk peningkatan dan pemerataan kualitas pendidikan di Indonesia yaitu dengan diaplikasikannya sistem zonasi pada Penerimaan Peserta Didik Baru atau disebut PPDB. Kecamatan Baleendah merupakan salah satu wilayah di Kabupaten Bandung dimana terdapat 2 Sekolah Menengah Pertama Negeri yaitu SMPN 1 Baleendah dan SMPN 2 Baleendah, yang sudah melaksanakan PPDB sejak tahun 2017, namun dalam pelaksanaan kebijakan sistem penerimaan peserta didik baru pada Tahun Pelajaran 2018/2019 belum sesuai dengan tujuan utama sistem zonasi PPDB 2019. Tujuan dari penelitian ini untuk menganalisis Bagaimana Implementasi Kebijakan Penerimaan Peserta Didik Baru Sistem Zonasi Tingkat Sekolah Menengah Pertama di Kecamatan Baleendah Kabupaten Bandung. Penelitian ini menggunakan model implementasi dari teori George C. Edward III. dalam Widodo, (2010: 96-110). Metode penelitian yang digunakan adalah metode penelitian deskriptif, dengan pendekatan kualitatif. Data diperoleh melalui studi pustaka, observasi partisipan, wawancara mendalam  dan dokumentasi. Hasil penelitian menunjukkan bahwa dalam pelaksanaannya Implementasi Kebijakan Penerimaan Peserta Didik Baru Sistem Zonasi Tingkat Sekolah Menengah Pertama di Kecamatan Baleendah Kabupaten Bandung terdapat beberapa faktor penghambat. Untuk mengatasi hambatan Dinas Pendidikan Kabupaten Bandung telah memastikan bahwa tidak ada lagi perbedaan kualitas dalam layanan pendidikan. Semakin dekat ke pusat, semakin berkualitaslah layanan pendidikan, baik dari sisi sarana, prasarana, dan ketersediaan guru.   Kata kunci: Implementasi kebijakan, penerimaan peserta didik baru, layanan pendidika

Capacities of Grassmann channels

A new class of quantum channels called Grassmann channels is introduced and their classical and quantum capacity is calculated. The channel class appears in a study of the two-mode squeezing operator constructed from operators satisfying the fermionic algebra. We compare Grassmann channels with the channels induced by the bosonic two-mode squeezing operator. Among other results, we challenge the relevance of calculating entanglement measures to assess or compare the ability of bosonic and fermionic states to send quantum information to uniformly accelerated frames.Comment: 33 pages, Accepted in Journal of Mathematical Physics; The role of the (fermionic) braided tensor product for quantum Shannon theory, namely capacity formulas, elucidated; The conclusion on the equivalence of Unruh effect for bosons and fermions for quantum communication purposes made clear and even more precis

A critical look at an Islamic Gold investment account

This article assesses an Islamic gold investment account offered by an Islamic bank in Malaysia and analyses its pros and cons. We look into the product’s relative advantages and disadvantages compare to some other Islamic deposit products and conventional gold accounts. In process of the assessment we also come across some Shari’ah compliance related issues and some practices which needs to be scrutinized from Shari’ah, economic and social perspectives. Overall, our findings suggest the account to be worthwhile investment instrument for long-term saving instrument and promising venture at times of boom in gold prices. However, the account is considered as a risky and unfavorable investment when gold price is on fall or if the customer intends to keep his deposits for a brief period. Finally, we pose some questions to the reader to ponder upon about some possible implication of the product for the Islamic bank, its customer or the society at large

One-dimensional quasi-relativistic particle in the box

Two-term Weyl-type asymptotic law for the eigenvalues of one-dimensional quasi-relativistic Hamiltonian (-h^2 c^2 d^2/dx^2 + m^2 c^4)^(1/2) + V_well(x) (the Klein-Gordon square-root operator with electrostatic potential) with the infinite square well potential V_well(x) is given: the n-th eigenvalue is equal to (n pi/2 - pi/8) h c/a + O(1/n), where 2a is the width of the potential well. Simplicity of eigenvalues is proved. Some L^2 and L^infinity properties of eigenfunctions are also studied. Eigenvalues represent energies of a `massive particle in the box' quasi-relativistic model.Comment: 40 pages, 4 figures; minor correction