Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical synthesis of oligodeoxyribonucleotides containing N3- and O4-carboxymethylthymidine and their formation in DNA

Humans are exposed to N-nitroso compounds from both endogenous and exogenous sources. Many N-nitroso compounds can be metabolically activated to give diazoacetate, which can result in the carboxymethylation of DNA. The remarkable similarity in p53 mutations found in human gastrointestinal tumors and in shuttle vector studies, where the human p53 gene-containing vector was treated with diazoacetate and propagated in yeast cells, suggests that diazoacetate might be an important etiological agent for human gastrointestinal tumors. The O6-carboxymethyl-2′-deoxyguanosine was previously detected in isolated DNA upon exposure to diazoacetate and in blood samples of healthy human subjects. The corresponding modifications of thymidine and 2′-deoxyadenosine have not been assessed, though significant mutations at A:T base pairs were found in the p53 tumor suppressor gene in human gastrointestinal tumors and in shuttle vector studies. To understand the implications of the carboxymethylation chemistry of thymidine in the observed mutations at A:T base pairs, here we synthesized authentic N3-carboxymethylthymidine (N3-CMdT) and O4-carboxymethylthymidine (O4-CMdT), incorporated them into DNA, and demonstrated, for the first time, that they were the major carboxymethylated derivatives of thymidine formed in calf thymus DNA upon exposure to diazoacetate. The demonstration of the formation of N3-CMdT and O4-CMdT in isolated DNA upon treatment with diazoacetate, together with the preparation of authentic oligodeoxyribonucleotide substrates housing these two lesions, laid the foundation for investigating the replication and repair of these lesions and for understanding their implications in the mutations observed in human gastrointestinal tumors.
Ecological and Evolutionary Processes Drive the Origin and Maintenance of Imperfect Mimicry

Although the forces behind the evolution of imperfect mimicry remain poorly studied, recent hypotheses suggest that relaxed selection on small-bodied individuals leads to imperfect mimicry. While evolutionary history undoubtedly affects the development of imperfect mimicry, ecological community context has largely been ignored and may be an important driver of imperfect mimicry. Here we investigate how evolutionary and ecological contexts might influence mimetic fidelity in Müllerian and Batesian mimicry systems. In Batesian hoverfly systems we find that body size is not a strong predictor of mimetic fidelity. However, in Müllerian velvet ants we find a weak positive relationship between body size and mimetic fidelity when evolutionary context is controlled for and a much stronger relationship between community diversity and mimetic fidelity. These results suggest that reduced selection on small-bodied individuals may not be a major driver of the evolution of imperfect mimicry and that other factors, such as ecological community context, should be considered when studying the evolution of imperfect mimicry.
Influence of the Processing of Magnesium Alloys AZ31 and ZE10 on the Sheet Formability at Elevated Temperature

The substitution of conventional materials such as aluminium alloys and steels with the lightest structural metal magnesium and its alloys can yield significant weight saving in the transportation industry and hence, reduce vehicle weight and greenhouse gas emissions. Producing magnesium sheets by conventional hot rolling is expensive due to the large number of rolling passes to final gauge and annealing steps at elevated temperatures between the rolling passes. Twin roll casting is a well established processing route for aluminium sheets which can reduce the necessary rolling passes to a bare minimum to reduce the production costs. This process is receiving increasing attention for the production of magnesium sheets. This study reveals first hand results of sheet metal forming experiments on magnesium sheets rolled from twin roll cast strip as well as conventional DC cast slabs. Two different alloys, AZ31 (Mg-3Al-1Zn-Mn) and rare earth element containing ZE10 (Mg-1Zn-RE) were investigated. It is known that these alloys show significant differences in the microstructure development during conventional rolling as a result of recrystallisation. For hot rolled AZ31, distinct textures are formed with the majority of basal planes oriented in the sheet plane and hence, unfavourably for basal slip. Conventionally rolled ZE10 commonly shows a much weaker texture. Forming limit diagrams are presented and discussed with respect to the initial texture of the sheets. Strain response to various strain paths and plastic anisotropy are evaluated. Results of twin roll cast sheets are compared with conventionally hot rolled sheet of the same alloys. Competitive formability can be achieved at 200°C for all tested sheets. While conventionally rolled sheets show a generally higher formability than their twin roll cast counterparts, ZE10 outperforms AZ31 for both processing routes.
Restricted jump interpolation in the d.c.e. degrees

We show that for any 2-computably enumerable Turing degree ${\bf l}$, any computably enumerable degree ${\bf a}$ and any Turing degree ${\bf s}$, if ${\bf l'=\boldsymbol{0}'}$, ${\bf l<a}$, ${\bf s\geq \boldsymbol{0}'}$, and ${\bf s}$ is c.e. in ${\bf a}$, then there is a 2-computably enumerable degree ${\bf x}$ with the following properties: ${\bf l<x<a}$; and ${\bf x'=s}$.
Tracing the Neural Carryover Effects of Interpersonal Anger on Resting-State fMRI in Men and Their Relation to Traumatic Stress Symptoms in a Subsample of Soldiers

Uncontrolled anger may lead to aggression and is common in various clinical conditions, including post traumatic stress disorder. Emotion regulation strategies may vary with some more adaptive and efficient than others in reducing angry feelings. However, such feelings tend to linger after anger provocation, extending the challenge of coping with anger beyond provocation. Task-independent resting-state (rs) fMRI may be a particularly useful paradigm to reveal neural processes of spontaneous recovery from a preceding negative emotional experience. We aimed to trace the carryover effects of anger on endogenous neural dynamics by applying a data-driven examination of changes in functional connectivity (FC) during rs-fMRI between before and after an interpersonal anger induction (N = 44 men). Anger was induced based on unfair monetary offers in a previously validated decision-making task. We calculated a common measure of global FC (gFC) which captures the level of FC between each region and all other regions in the brain, and examined which brain regions manifested changes in this measure following anger. We next examined the changes in all functional connections of each individuated brain region with all other brain regions to reveal which connections underlie the differences found in the gFC analysis of the previous step. We subsequently examined the relation of the identified neural modulations in the aftermath of anger with state- and trait- like measures associated with anger, including brain structure, and in a subsample of designated infantry soldiers (N = 21), with levels of traumatic stress symptoms (TSS) measured 1 year later following combat-training. The analysis pipeline revealed an increase in right amygdala gFC in the aftermath of anger and specifically with the right inferior frontal gyrus (IFG). We found that the increase in FC between the right amygdala and right IFG following anger was positively associated with smaller right IFG volume, higher trait-anger level and among soldiers with more TSS. Moreover, higher levels of right amygdala gFC at baseline predicted less reported anger during the subsequent anger provocation. The results suggest that increased amygdala-IFG connectivity following anger is associated with maladaptive recovery, and relates to long-term development of stress symptomatology in a subsample of soldiers.
Are the High-growth Recovery Periods Over?

We present evidence about the loss of the so-called "plucking effect", that is, a high-growth phase of the cycle typically observed at the end of recessions. This result matches the popular belief, presented informally by different authors, that the current recession will have permanent effects, or that the current recession will have an L shape versus the old-time recessions that have always had a V shape. Furthermore, we show that the loss of the "plucking effect" can explain part of the Great Moderation. We postulate that these two phenomena may be due to changes in inventory management brought about by improvements in information and communications technologies.
Hollywood 3D: Recognizing Actions in 3D Natural Scenes

Action recognition in unconstrained situations is a difficult task, suffering from massive intra-class variations. It is made even more challenging when complex 3D actions are projected down to the image plane, losing a great deal of information. The recent emergence of 3D data, both in broadcast content, and commercial depth sensors, provides the possibility to overcome this issue. This paper presents a new dataset, for benchmarking action recognition algorithms in natural environments, while making use of 3D information. The dataset contains around 650 video clips, across 14 classes. In addition, two state of the art action recognition algorithms are extended to make use of the 3D data, and five new interest point detection strategies are also proposed, that extend to the 3D data. Our evaluation compares all 4 feature descriptors, using 7 different types of interest point, over a variety of threshold levels, for the Hollywood3D dataset. We make the dataset including stereo video, estimated depth maps and all code required to reproduce the benchmark results, available to the wider community.
Grieving in the Muscogee Creek Tribe

A qualitative, collective case study explores grieving in the Muscogee Creek tribe. Data from interviews with 27 participants, all adult members of the tribe, reveal tendencies in patterns of grieving. Commonalities include (a) individual strength and certainty of recovery; (b) focus on giving to others in the family and coping as a family unit; and (c) support mainly received from family. Cultural factors of belief in nature's balance, family, community, and Indian medicine influence the meaning Creeks associate with death, which, in turn, contributes to grieving patterns.
Immunocytochemical localization of nuclear estrogen receptors and progestin receptors within the rat dorsal raphe nucleus

Estradiol and progesterone modulate central serotonergic activity; however, the mechanism(s) of action remain unclear. Recently, estradiol‐induced progestin receptors (PRs) have been localized within the majority of serotonin (5‐HT) neurons in the female macaque dorsal raphe nucleus (DRN; Bethea [1994] Neuroendocrinology 60:50–61). In the present study, we investigated whether estrogen receptors (ERs) and/or PRs exist within 5‐HT and/or non‐5‐HT cells in the female and male rat DRN and whether estradiol treatment alters the expression of these receptors. Young adult female and male Sprague‐Dawley rats were gonadectomized, and 1 week later, half of the animals received a subcutaneous Silastic implant of estradiol‐17β. Animals were transcardially perfused 2 days later with acrolein and paraformaldehyde, and sequential dual‐label immunocytochemistry was performed on adjacent sections by using either a PR antibody or an ERα antibody. This was followed by an antibody to either the 5‐HT‐synthesizing enzyme, tryptophan hydroxylase (TPH), or to the astrocytic marker, glial fibrillary acidic protein (GFAP). Cells containing immunoreactivity (ir) for nuclear ERs or PRs were identified within the rat DRN in a region‐specific distribution in both sexes. No colocalization of nuclear ER‐ir or PR‐ir with cytoplasmic TPH‐ir or GFAP‐ir was observed in either sex or treatment, indicating that the steroid target cells are neither 5‐HT neurons nor astrocytes. Females were found to have approximately 30% more PR‐labeled cells compared with males throughout the DRN (P < 0.05), but no sex difference was detected in the number of neurons demonstrating ER‐ir. In both sexes, 2 days of estradiol exposure decreased the number of cells with ER‐ir, whereas it greatly increased the number of cells containing PR‐ir in several DRN regions (P < 0.005). Collectively, these findings demonstrate the existence of nonserotonergic cells that contain nuclear ERs or PRs within the female and male rat DRN, including estradiol‐inducible PRs. These findings point to a species difference in ovarian steroid regulation of 5‐HT activity between the macaque and the rat, perhaps transsynaptically via local neurons in the rat brain. J. Comp. Neurol. 391:322–334, 1998. © 1998 Wiley‐Liss, Inc.
In Candida albicans, phosphorylation of Exo84 by Cdk1-Hgc1 is necessary for efficient hyphal extension

Candida albicans hyphae continue to grow throughout mitosis, and phosphorylation of Exo84 by Cdk is necessary for efficient hyphal growth. In contrast, phosphorylation of Exo84 by Cdk halts cell growth in Saccharomyces cerevisiae. The location of Cdk1 target sites in Exo84 explains how phosphoregulation mediates these different patterns of growth.
Deciphering mobile search patterns: a study of Yahoo! mobile search queries

In this paper we study the characteristics of search queries submitted from mobile devices using various Yahoo! one-Search applications during a 2 months period in the second half of 2007, and report the query patterns derived from 20 million English sample queries submitted by users in US, Canada, Europe, and Asia. We examine the query distribution and topical categories the queries belong to in order to find new trends. We compare and contrast the search patterns between US vs international queries, and between queries from various search interfaces (XHTML/WAP, java widgets, and SMS). We also compare our results with previous studies wherever possible, either to confirm previous findings, or to find interesting differences in the query distribution and pattern.
Bugs as deviant behavior: a general approach to inferring errors in systems code

A major obstacle to finding program errors in a real system is knowing what correctness rules the system must obey. These rules are often undocumented or specified in an ad hoc manner. This paper demonstrates techniques that automatically extract such checking information from the source code itself, rather than the programmer, thereby avoiding the need for a priori knowledge of system rules.The cornerstone of our approach is inferring programmer "beliefs" that we then cross-check for contradictions. Beliefs are facts implied by code: a dereference of a pointer, p, implies a belief that p is non-null, a call to "unlock(1)" implies that 1 was locked, etc. For beliefs we know the programmer must hold, such as the pointer dereference above, we immediately flag contradictions as errors. For beliefs that the programmer may hold, we can assume these beliefs hold and use a statistical analysis to rank the resulting errors from most to least likely. For example, a call to "spin_lock" followed once by a call to "spin_unlock" implies that the programmer may have paired these calls by coincidence. If the pairing happens 999 out of 1000 times, though, then it is probably a valid belief and the sole deviation a probable error. The key feature of this approach is that it requires no a priori knowledge of truth: if two beliefs contradict, we know that one is an error without knowing what the correct belief is.Conceptually, our checkers extract beliefs by tailoring rule "templates" to a system --- for example, finding all functions that fit the rule template "a must be paired with b. " We have developed six checkers that follow this conceptual framework. They find hundreds of bugs in real systems such as Linux and OpenBSD. From our experience, they give a dramatic reduction in the manual effort needed to check a large system. Compared to our previous work [9], these template checkers find ten to one hundred times more rule instances and derive properties we found impractical to specify manually.
Reactivation of herpes simplex virus type 1 in patients with Bell's palsy

Reactivation of herpes simplex virus type 1 (HSV‐1) has been implicated in the pathogenesis of idiopathic peripheral facial palsy (Bell's palsy). The present study used the polymerase chain reaction (PCR) to analyze the saliva of patients with Bell's palsy for the presence of shed HSV‐1. The study involved 47 patients with Bell's palsy, 24 patients with Ramsay Hunt syndrome, and 16 healthy HSV‐seropositive volunteers. HSV‐1 DNA was not detected in the saliva samples from HSV‐seronegative patients. The prevalence of shed HSV‐1 in patients with Bell's palsy (50%) was significantly higher than that in healthy volunteers (19%, p<0.05). When saliva samples were tested within 7 days after the onset of palsy, the prevalence of shed HSV‐1 in patients with Bell's palsy (40%) was significantly higher than that in patients with Ramsay Hunt syndrome (7%, p<0.05). Furthermore, HSV‐1 usually became undetectable by the second week after the onset of Bell's palsy when HSV‐1 was detected during the acute phase of the disease. These findings strongly suggest that reactivation of HSV‐1 is involved in the pathogenesis Bell's palsy, and indicate that PCR is a useful tool for early diagnosis of HSV‐1 reactivation in patients with Bell's palsy. J. Med. Virol. 54:162–166, 1998. © 1998 Wiley‐Liss, Inc.
Multiple Rieske Proteins Enable Short- and Long-term Light Adaptation of Synechocystis sp. PCC 6803*

In contrast to eukaryotes, most cyanobacteria contain several isoforms of the Rieske iron-sulfur protein, PetC, resulting in heterogeneity in the composition of the cytochrome b6f complexes. Of three isoforms in the mesophilic cyanobacterium Synechocystis PCC 6803, PetC1 is the major Rieske protein in the cytochrome b6f complex, whereas the physiological function of PetC2 and PetC3 is still uncertain. Comparison of wild type and various petC-deficient strains under selected light conditions revealed distinct functional differences: high-light exposure of wild type cells resulted in a significantly enhanced petC2 transcript level, whereas a ΔpetC1 mutant showed a low cytochrome b6f content, low electron flux, and a considerably increased accumulation of cytochrome-bd oxidase. In contrast to wild type and ΔpetC1, ΔpetC2 and ΔpetC3 strains still grew fast under high-light conditions although all three Rieske proteins are required for maximal electron transport rates. Although the presence of PetC3 appears to be required for activation of the cyclic electron transport, state transitions were more effective in the absence of PetC2 and/or PetC3. In summary, our data suggest defined roles of the various PetC proteins in short- and long-term light adaptation.
Intravenous Thrombolysis in German Stroke Units before and after Regulatory Approval of Recombinant Tissue Plasminogen Activator

Background: Intravenous thrombolysis with recombinant tissue plasminogen activator (rt-PA) within 3 h after onset of focal cerebral ischemia was approved in Germany in August 2000. Methods: 11 neurology departments with acute stroke units participated in the German Stroke Study Collaboration before (n = 2,925) and after (n = 3,204) approval of rt-PA in Germany and consecutively registered all patients admitted within 24 h following acute ischemic stroke. Results: Frequency of intravenous thrombolysis in patients admitted within 24 h after symptom onset increased from 4.8% before approval to 7.9% after approval of rt-PA. Among patients treated with rtPA, age increased significantly and the delay between symptom onset and imaging was significantly shorter in the second study period. Conclusions: The observed improvement in management and quantity of intravenous thrombolysis may be explained by greater experience and greater legal security following regulatory approval of rtPA.
SoCIN: a parametric and scalable network-on-chip

Networks-on-chip (NoCs) interconnection architectures, to be used in future billion-transistor systems-on-chip (SoCs), meet the major communication requirements of these systems, offering, at the same time, reusability, scalability and parallelism in communication. Furthermore, they cope with other issues like power constraints and clock distribution. Currently, there are a number of research works which explore different features of NoCs. In this paper, we present SoCIN, a scalable network based on a parametric router architecture to be used in the synthesis of customized low cost NoCs. The architecture of SoCIN and its router are described, and some synthesis results are presented.
PALEOECOLOGY OF FOREST ENVIRONMENTS THROUGH TIME: EVIDENCE FROM STABLE ISOTOPES OF MAMMALIAN HERBIVORES IN THE NEW WORLD

3 To my brother, Craig 4 ACKNOWLEDGMENTS I would like to thank the members of my graduate committee for all their support over the course of the past six years. Each of my committee members helped me to mature as a scientist, and for that I am very grateful: I truly appreciate the patience shown by Dr. Luciano Brocchieri as he assisted me in developing my programing skills, the open door to Dr. Edward Braun's office (where I could always receive impromptu advice), the big picture perspective and encouragement that Dr. Jamie Gilooly always provided, the guidance in science and life that Dr. Michael Miyamoto offered, and the amazing opportunity provided to me by Dr. Charles Baer. I can't find the words to convey my appreciation for the friendship and support that Charlie has provided, nor can I begin to express how much it means to me that he believed in me through this whole process. I would like to thank my best friend and wife, Gigi Ostrow, for always being there to support me over the past six years. Also, I would also like to thank all my friends for their support throughout my education. I was very fortunate to have the help of my brother Keith Salomon always was there to help me with any computer programing challenges I came across. Finally, I would like to thank my mother and father for everything they have done for me throughout my entire life. Without their love and support none of this would have been possible.
Cyanide bystander effect of the linamarase/linamarin killer‐suicide gene therapy system

The killer‐suicide system linamarase/linamarin (lis/lin) uses the plant gene linamarase (β‐glucosidase) to convert the cyanogenic glucoside substrate, linamarin, into glucose and cyanide. We have studied the bystander effect associated with this new system mediated by the production of the cyanide ion that diffuses freely across membranes.