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The present article posits constructive technology assessment as the dominant perspective of societal embedding practices in the technical development process by the high-speed train manufacturing industry, resulting from a research study conducted in 2011 (Moretto 2011). The article covers the main elements of the study, being the high-speed train manufacturing industry’s strategic intelligence, technology pattern, knowledge exchange, technology trajectories; and finally presents the arguments justifying constructive technology assessment as the dominant approach.

Several lines of recent evidence support a role for chromatin in splicing regulation. Here, we show that splicing can also contribute to histone modification, which implies bidirectional communication between epigenetic mechanisms and RNA processing. Genome-wide analysis of histone methylation in human cell lines and mouse primary T cells reveals that intron-containing genes are preferentially marked with histone H3 Lys36 trimethylation (H3K36me3) relative to intronless genes. In intron-containing genes, H3K36me3 marking is proportional to transcriptional activity, whereas in intronless genes, H3K36me3 is always detected at much lower levels. Furthermore, splicing inhibition impairs recruitment of H3K36 methyltransferase HYPB (also known as Setd2) and reduces H3K36me3, whereas splicing activation has the opposite effect. Moreover, the increase of H3K36me3 correlates with the length of the first intron, consistent with the view that splicing enhances H3 methylation. We propose that splicing is mechanistically coupled to recruitment of HYPB/Setd2 to elongating RNA polymerase II.

This paper presents StarTM , an automatic verification tool for transactional memory Java programs executing under relaxed isolation levels. We certify which transactions in a program are safe to execute under Snapshot Isolation without triggering the write-skew anomaly, opening the way to run-time optimizations that may lead to considerable performance enhancements.
Our tool builds on a novel shape analysis technique based on Separation Logic to statically approximate the read- and write-sets of a transactional memory Java program. This technique is particularly challenging due to the presence of dynamically allocated memory.
We implement our technique and apply our tool to a set of intricate examples. We corroborate known results, certifying some of the examples for safe execution under Snapshot Isolation by proving the absence of write-skew anomalies. In other cases we identify transactions that potentially trigger the write-skew anomaly.

Multiheme cytochromes c are important in electron transfer pathways in reduction of both soluble and insoluble Fe(III) by Geobacter sulfurreducens. We determined the crystal structure at 3.2 Å resolution of the first dodecaheme cytochrome c (GSU1996) along with its N-terminal and C-terminal hexaheme fragments at 2.6 and 2.15 Å resolution, respectively. The macroscopic reduction potentials of the full-length protein and its fragments were measured. The sequence of GSU1996 can be divided into four c7-type domains (A, B, C and D) with homology to triheme cytochromes c7. In cytochromes c7 all three hemes are bis–His coordinated, whereas in c7-type domains the last heme is His–Met coordinated. The full-length GSU1996 has a 12 nm long crescent shaped structure with the 12 hemes arranged along a polypeptide to form a “nanowire” of hemes; it has a modular structure. Surprisingly, while the C-terminal half of the protein consists of two separate c7-type domains (C and D) connected by a small linker, the N-terminal half of the protein has two c7-type domains (A and B) that form one structural unit. This is also observed in the AB fragment. There is an unexpected interaction between the hemes at the interface of domains A and B, which form a heme-pair with nearly parallel stacking of their porphyrin rings. The hemes adjacent to each other throughout the protein are within van der Waals distance which enables efficient electron exchange between them. For the first time, the structural details of c7-type domains from one multiheme protein were compared.

Em caso de falha abrupta de um sistema, é imperativo garantir a consistência do Sistema de Ficheiros (SF). Actualmente existem várias solu{\c c}ões que visam garantir que tanto os dados como os metadados do SF se encontram num estado consistente, mas que não contemplam a garantia de consistência dos dados do ponto de vista das aplica{\c c}ões. Por exemplo, aplica{\c c}ões que pretendam alterar vários ficheiros de configura{\c c}ão terão de encontrar mecanismos para garantir que, ou todos os ficheiros são devidamente alterados, ou nenhum o é, evitando assim que numa situa{\c c}ão de falha o conteúdo dos ficheiros fique inconsistente. Do ponto de vista da aplica{\c c}ão, pode não ser simples implementar este comportamento sobre um SF t{\'ıpico; e pode também não ser razoável utilizar um Sistema de Gestão de Bases de Dados (SGBD), que oferece propriedades ACID. Neste artigo propomos, testamos e avaliamos uma integra{\c c}ão das propriedades ACID num SF. Partindo do suporte para snapshots do sistema de ficheiros Btrfs, oferece-se uma semântica transaccional às aplica{\c c}ões que operam sobre volumes (sub-árvores) do SF, sem comprometer a semântica POSIX do SF.

“Theory and Practice” of TA, which is referred to in the title of this journal “TATuP”, is usually addressed as a question of TA research. But science is more than research: the field of teaching requires just as much attention, both practically and theoretically. Therefore, a mere collection of individual teaching experiences and best practice examples does not provide a strong enough basis to discuss questions of TA teaching, these must also be embedded in a theoretical context and discussed in their relation to research. In this special issue, we aim to contribute to a combination of theoretical and practical approaches to the relation of TA and “Bildung”.

The present work proposes the development of a bio-battery composed by an ultrathin monolithic structure of an electrospun cellulose acetate membrane, over which was deposited metallic thin film electrodes by thermal evaporation on both surfaces. The electrochemical characterization of the bio-batteries was performed under simulated body fluids like sweat and blood plasma [salt solution–0.9% (w/w) NaCl]. Reversible electrochemical reactions were detected through the cellulose acetate structure. Thus, a stable electrochemical behavior was achieved for a bio-battery with silver and aluminum thin films as electrodes. This device exhibits the ability to supply a power density higher than 3 muW cm(-2). Finally, a bio-battery prototype was tested on a sweated skin, demonstrating the potential of applicability of this bio-device as a micropower source.

The two-decade long history of events relating object-oriented programming, the development of persistence and transactional support, and the aggregation of multiple nodes in a single-system image cluster, appears to convey the following conclusion: programmers ideally would develop and deploy applications against a single shared global memory space (heap of objects) of mostly unbounded capacity, with implicit support for persistence and concurrency, transparently backed by a possibly large number of clustered physical machines.

In this paper, we propose a new approach to the design of OODB systems for Java applications: (O3)2 (pronounced ozone squared). It aims at providing to developers a single-system image of virtually unbounded object space/heap with support for object persistence, object querying, transactions and concurrency enforcement, backed by a cluster of multi-core machines with Java VMs that is kept transparent to the user/developer. It is based on an existing persistence framework (ozone-db) and the feasibility and performance of our approach has been validated resorting to the OO7 benchmark.

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Several decades ago, the file system was the container of choice for large bulks of related information, kept in hundreds of files, and relying on applications specifically created to handle them. These configurations weren't scalable and could easily become difficult to maintain, leading to the development and adoption of Database Management Systems (DBMS). These systems, capable of efficiently handling vast amounts of data, allowed heavy concurrency without requiring the programmer to deal with concurrency-control mechanisms, by encapsulating operations within transactions.
The properties of Transactions rapidly became an object of desire by many, and efforts to bring them to general-purpose programming environments began. In recent years there have been breakthroughs in bringing the transactional semantics to memory, using Software Transactional Memory (STM), providing abstractions to concurrency-control on the application-level. However, STM failed to meet some expectations, specially regarding I/O operations, forcing the abstraction to go deeper in the system: directly to the file system.
In this document we shall discuss file systems in general, their properties and common structure, although focusing in those with transactional or versioning capabilities. Later on, we will present our proposed enhancement of an existing Linux file system (Btrfs), in order to offer transactional semantics to applications, while detecting potential conflicts between concurrent flows of execution and reconciling their changes whenever possible.

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AraL from Bacillus subtilis is a member of the ubiquitous haloalkanoate dehalogenase superfamily. The araL gene has been cloned, over-expressed in Escherichia coli and its product purified to homogeneity. The enzyme displays phosphatase activity, which is optimal at neutral pH (7.0) and 65 °C. Substrate screening and kinetic analysis showed AraL to have low specificity and catalytic activity towards several sugar phosphates, which are metabolic intermediates of the glycolytic and pentose phosphate pathways. On the basis of substrate specificity and gene context within the arabinose metabolic operon, a putative physiological role of AraL in the detoxification of accidental accumulation of phosphorylated metabolites has been proposed. The ability of AraL to catabolize several related secondary metabolites requires regulation at the genetic level. In the present study, using site-directed mutagenesis, we show that the production of AraL is regulated by a structure in the translation initiation region of the mRNA, which most probably blocks access to the ribosome-binding site, preventing protein synthesis. Members of haloalkanoate dehalogenase subfamily IIA and IIB are characterized by a broad-range and overlapping specificity anticipating the need for regulation at the genetic level. We provide evidence for the existence of a genetic regulatory mechanism controlling the production of AraL.