Faking Fairness via Stealthily Biased Sampling

Auditing fairness of decision-makers is now in high demand. To respond to this social demand, several fairness auditing tools have been developed. The focus of this study is to raise an awareness of the risk of malicious decision-makers who fake fairness by abusing the auditing tools and thereby deceiving the social communities. The question is whether such a fraud of the decision-maker is detectable so that the society can avoid the risk of fake fairness. In this study, we answer this question negatively. We specifically put our focus on a situation where the decision-maker publishes a benchmark dataset as the evidence of his/her fairness and attempts to deceive a person who uses an auditing tool that computes a fairness metric. To assess the (un)detectability of the fraud, we explicitly construct an algorithm, the stealthily biased sampling, that can deliberately construct an evil benchmark dataset via subsampling. We show that the fraud made by the stealthily based sampling is indeed difficult to detect both theoretically and empirically.Comment: Accepted at the Special Track on AI for Social Impact (AISI) at AAAI202

Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors

<p>Abstract</p> <p>Background</p> <p>In addition to structural domains, most eukaryotic proteins possess intrinsically disordered (ID) regions. Although ID regions often play important functional roles, their accurate identification is difficult. As human transcription factors (TFs) constitute a typical group of proteins with long ID regions, we regarded them as a model of all proteins and attempted to accurately classify TFs into structural domains and ID regions. Although an extremely high fraction of ID regions besides DNA binding and/or other domains was detected in human TFs in our previous investigation, 20% of the residues were left unassigned. In this report, we exploit the generally higher sequence divergence in ID regions than in structural regions to completely divide proteins into structural domains and ID regions.</p> <p>Results</p> <p>The new dichotomic system first identifies domains of known structures, followed by assignment of structural domains and ID regions with a combination of pre-existing tools and a newly developed program based on sequence divergence, taking un-aligned regions into consideration. The system was found to be highly accurate: its application to a set of proteins with experimentally verified ID regions had an error rate as low as 2%. Application of this system to human TFs (401 proteins) showed that 38% of the residues were in structural domains, while 62% were in ID regions. The preponderance of ID regions makes a sharp contrast to TFs of <it>Escherichia coli </it>(229 proteins), in which only 5% fell in ID regions. The method also revealed that 4.0% and 11.8% of the total length in human and <it>E. coli </it>TFs, respectively, are comprised of structural domains whose structures have not been determined.</p> <p>Conclusion</p> <p>The present system verifies that sequence divergence including information of unaligned regions is a good indicator of ID regions. The system for the first time estimates the complete fractioning of structured/un-structured regions in human TFs, also revealing structural domains without homology to known structures. These predicted novel structural domains are good targets of structural genomics. When applied to other proteins, the system is expected to uncover more novel structural domains.</p

Acclimation of photosynthetic properties in psychrophilic diatom isolates under different light intensities

Acclimation of growth and photosynthetic properties was examined for diatom strains, isolated from Saroma Ko lagoon (44°N, 144°E) in early spring, under different light intensities at 1℃. The relatively high specific growth constants under low irradiances were recognized for both Chaetoceros sp. and Thalassiosira sp. Further examination of photosynthesis in Chaetoceros sp. showed that growth under low irradiance caused an increase in the photosynthetic effciency for Chl α-specific rate of gross O_2 evolution (α^B) and a decrease in the Chl α-specific rate of dark O_2 respiration (R_d^B), which was extrapolated from the initial slope of net O_2 evolution rate vs. irradiance curve. These changes explain the low light compensation point for net photosynthetic O_2 evolution (I_c) and the high efficiency for growth under low irradiance conditions. Neither Chl α-specific amounts of light-harvesting pigments, such as fucoxanthin and Chl c, nor cellular content of Chl α, but Chl α-specific amount of diadinoxanthin was varied by the change in irradiance condition. The increase of α^B under low growth irradiance corresponded with a decrease in the amount of diadinoxanthin relative to Chl α. However, the Chl α-specific maximum photosynthetic rate (P_m^B) was retained at the same level and photoinhibition could not be observed under illumination up to &acd;800μE m^ s^. The light intensity at which photosynthesis was light-saturated (I_k, =P_m^B/α^B) was much higher than the incident growth irradiances (76 and 88μE m^ s^ under the growth irradiances of 11 and 42 μE m^ s^, respectively), although the value of I_k for the former was significantly smaller (t-test, P<0.001) than that for the latter. Thus, the capacity of photochemical reaction around photosystems seems to remain large even under low irradiance. These properties may indicate that the diatom cells could efficiently utilize light-energy under large variation of irradiance even on a short time-scale

学会抄録

<p>A. The average number of interactions decomposed by the interaction partners in 7 categories: NP, CP, MP, NCP, CMP, NCMP, and others. The full size view is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156455#pone.0156455.s003" target="_blank">S2 Fig</a>. B. The Venn diagram representing the interaction of NP with NCP. In total, 2,498 NP were analyzed. The NP with intra-interactions and interacting with NCP are shown by the two circles in the box. The intersection of two circles represents the shared interaction partners. Among these proteins, 1,250 NP neither intra-interact nor interact with NCP. C. The summary of interactions in terms of interaction partners. S symbols indicate that the interaction is rich (at least 0.6 interaction partners) between the protein (the left column) and the interaction partners (the top row), and the interaction partners are shared (at least 0.5) with the intra-interactions of partner proteins (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156455#pone.0156455.s010" target="_blank">S6 Table</a>). For other symbols, see the bottom of the panel.</p

Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures

金沢大学医薬保健研究域保健学系It is known that in thermophiles the G+C content of ribosomal RNA linearly correlates with growth temperature, while that of genomic DNA does not. Although the G+C contents (singlet) of the genomic DNAs of thermophiles and methophiles do not differ significantly, the dinucleotide (doublet) compositions of the two bacterial groups clearly do. The average amino acid compositions of proteins of the two groups are also distinct. Based on these facts, we here analyzed the DNA and protein compositions of various bacteria in terms of the optimal growth temperature (OGT). Regression analyses of the sequence data for thermophilic, mesophilic and psychrophilic bacteria revealed good linear relationships between OGT and the dinucleotide compositions of DNA, and between OGT and the amino acid compositions of proteins. Together with the above-mentioned linear relationship between ribosomal RNA and OGT, the DNA and protein compositions can be regarded as thermostability measures for RNA, DNA and proteins, covering a wide range of temperatures. Both the DNA and proteins of psychrophiles apparently exhibit characteristics diametrically opposite to those of thermophiles. The physicochemical parameters of dinucleotides suggested that supercoiling of DNA is relevant to its thermostability. Protein stability in thermophiles is realized primarily through global changes that increase charged residues (i.e., Glu, Arg, and Lys) on the molecular surface of all proteins. This kind of global change is attainable through a change in the amino acid composition coupled with alterations in the DNA base composition. The general strategies of thermophiles and psychrophiles for adaptation to higher and lower temperatures, respectively, that are suggested by the present study are discussed

Biological investigations of the Antarctic ice sheet: review, problems and projects

The Antarctic Icecap has attracted considerable attention of scientists for many years. Many microbiological and general biological studies of the ground surface, snow and glacial cover have been performed. In recent decades, it has been discovered that the Antarctic ice sheet is a unique depository of paleoclimatic and paleomicrobiological information that reflects previous ecological events on our planet. Thus, dust particles, spores, plant pollen, and different microorganisms, which were brought onto the glacier surface by wind, appear to be gradually buried in the glacier layers and preserved in the frozen state for hundreds thousands years. These investigations have become especially important in the era of space research, many scientists consider the Antarctic as the most appropriate model to solve some methodical problems in astrobiology. Further developments and improvements of drilling methods have made it possible to penetrate into the deepest levels of the Antarctic Icecap, including the lower layers of so-called accretion ice above the sub-glacial Lake Vostok. The initial glaciological and microbiological investigations were mainly focused on the glacier ice and gave very useful information on the history of the Earth\u27s climate and the distribution of dust particles and microorganisms in the ice sheet during different periods. However, studies of the deep accretion ice and the sub-glacial Lake Vostok are expected to provide more insight into relict microbial forms and give rise to new investigations of the Antarctic ice cover. These works should include searches for microbial life in the accretion ice and Lake Vostok, and requires new biological techniques, new multidisciplinary approaches and international cooperation. Nowadays, biological investigations of the Earth\u27s polar regions are of paramount importance in view of current ecological problems. Of no less significance is the search for possible extraterrestrial life, since permafrost and glaciers are widely spread in the Universe; this is why, researchers have paid great attention to the Antarctic as a model for astrobiology

Computational Prediction of O-linked Glycosylation Sites That Preferentially Map on Intrinsically Disordered Regions of Extracellular Proteins

O-glycosylation of mammalian proteins is one of the important posttranslational modifications. We applied a support vector machine (SVM) to predict whether Ser or Thr is glycosylated, in order to elucidate the O-glycosylation mechanism. O-glycosylated sites were often found clustered along the sequence, whereas other sites were located sporadically. Therefore, we developed two types of SVMs for predicting clustered and isolated sites separately. We found that the amino acid composition was effective for predicting the clustered type, whereas the site-specific algorithm was effective for the isolated type. The highest prediction accuracy for the clustered type was 74%, while that for the isolated type was 79%. The existence frequency of amino acids around the O-glycosylation sites was different in the two types: namely, Pro, Val and Ala had high existence probabilities at each specific position relative to a glycosylation site, especially for the isolated type. Independent component analyses for the amino acid sequences around O-glycosylation sites showed the position-specific existences of the identified amino acids as independent components. The O-glycosylation sites were preferentially located within intrinsically disordered regions of extracellular proteins: particularly, more than 90% of the clustered O-GalNAc glycosylation sites were observed in intrinsically disordered regions. This feature could be the key for understanding the non-conservation property of O-glycosylation, and its role in functional diversity and structural stability

Impaired Anaphylactic Responses with Intact Sensitivity to Endotoxin in Mice Lacking a Platelet-activating Factor Receptor

Platelet-activating factor (PAF) is a potent phospholipid mediator with diverse biological activities in addition to its well-known ability to stimulate platelet aggregation. Pharmacologic studies had suggested a role for PAF in pregnancy, neuronal cell migration, anaphylaxis, and endotoxic shock. Here we show that disruption of the PAF receptor gene in mice caused a marked reduction in systemic anaphylactic symptoms. Unexpectedly, however, the PAF receptor–deficient mice developed normally, were fertile, and remained sensitive to bacterial endotoxin. These mutant mice clearly show that PAF plays a dominant role in eliciting anaphylaxis, but that it is not essential for reproduction, brain development, or endotoxic shock