bluuebunny/crossref_metadata_2025 huggingface dataset:
Using the Suicide Index Score to Predict Treatment Outcomes among Psychiatric Inpatients
Authors: Lento René M. , Ellis Thomas E. , Hinnant Benjamin J. , Jobes David A.
Published: June 2013

For many suicidal people, the desire to die is moderated by a competing desire to live. This study aimed to demonstrate the ability of a wish‐to‐live versus wish‐to‐die index score to measure ambivalence and trichotomize suicidal inpatients into distinct stratified risk groups. Analyses revealed that index scores calculated for patients at treatment start significantly discriminated among the groups at index and uniquely predicted suicidal ideation, hopelessness, and depression scores across treatment. On average, patients with wish‐to‐live and wish‐to‐die orientations resolved suicidal ideation by discharge. Changes in suicidal ideation among ambivalently oriented patients were more variable. Clinical and research implications are discussed.
Using a periclinal chimera to unravel layer‐specific gene expression in plants
Authors: Filippis Ioannis , Lopez‐Cobollo Rosa , Abbott James , Butcher Sarah , Bishop Gerard J.
Published: June 2013

Plant organs are made from multiple cell types, and defining the expression level of a gene in any one cell or group of cells from a complex mixture is difficult. Dicotyledonous plants normally have three distinct layers of cells, L1, L2 and L3. Layer L1 is the single layer of cells making up the epidermis, layer L2 the single cell sub‐epidermal layer and layer L3 constitutes the rest of the internal cells. Here we show how it is possible to harvest an organ and characterise the level of layer‐specific expression by using a periclinal chimera that has its L1 layer from Solanum pennellii and its L2 and L3 layers from Solanum lycopersicum. This is possible by measuring the level of the frequency of species‐specific transcripts. RNA‐seq analysis enabled the genome‐wide assessment of whether a gene is expressed in the L1 or L2/L3 layers. From 13 277 genes that are expressed in both the chimera and the parental lines and with at least one polymorphism between the parental alleles, we identified 382 genes that are preferentially expressed in L1 in contrast to 1159 genes in L2/L3. Gene ontology analysis shows that many genes preferentially expressed in L1 are involved in cutin and wax biosynthesis, whereas numerous genes that are preferentially expressed in L2/L3 tissue are associated with chloroplastic processes. These data indicate the use of such chimeras and provide detailed information on the level of layer‐specific expression of genes.
Molecular Mass Transportation Via Carbon Nanoscrolls
Authors: Huang Yinjun , Li Teng
Published: June 2013

The open topology of a carbon nanoscroll (CNS) inspires potential applications such as high capacity hydrogen storage. Enthusiasm for this promising application aside, one crucial problem that remains largely unexplored is how to shuttle the hydrogen molecules adsorbed inside CNSs. Using molecular dynamics simulations, we demonstrate two effective transportation mechanisms of hydrogen molecules enabled by the torsional buckling instability of a CNS and the surface energy induced radial shrinkage of a CNS. As these two mechanisms essentially rely on the nonbonded interactions between the hydrogen molecules and the CNS, it is expected that similar mechanisms could be applicable to the transportation of molecular mass of other types, such as water molecules, deoxyribonucleic acids (DNAs), fullerenes, and nanoparticles.
Hierarchical Structure and Properties of Graphene Oxide Papers
Authors: Wood Charles D. , Palmeri Marc J. , Putz Karl W. , An Zhi , Nguyen SonBinh T. , Catherine Brinson L.
Published: June 2013

The mechanical properties of graphene oxide papers have attracted significant attention in recent years due to their high stiffness and tough behavior. While the structural feature most commonly characterized is the nanosheet spacing, there is a hierarchical structure, which is likely responsible for the impressive mechanical properties. In this paper, we examine the structure of graphene oxide papers on several length scales using novel techniques to distinguish between lamellae and a newly defined feature, termed “super-lamellae.” The differentiation between these intermediate features provides context to the previously observed mechanical response and fracture surfaces of graphene oxide papers, particularly under uniaxial tension.
On the Fracture of Supported Graphene Under Pressure
Authors: Song Zhigong , Xu Zhiping , Huang Xianliang , Kim Ji-Yeun , Zheng Quanshui
Published: June 2013

We explore here the structural stability and fracture of supported graphene sheets under pressure loadings normal to the sheets by performing molecular dynamics simulations. The results show that, in absence of defects, supported graphene deforms into an inverse bubble shape and fracture is nucleated at the supported edges. The critical pressure decreases from ideal tensile strength of graphene in biaxial tension as the size of supporting pores increases. When nanoscale holes are created in the suspended region of graphene, the critical pressure is further lowered with the area of nanoholes, with additional dependence on their shapes. The results are explained by analyzing the deformed profile of graphene sheets under pressure and the stress state.
On the use of biomathematical models in patient‐specific IMRT dose QA
Authors: Zhen Heming , Nelms Benjamin E. , Tomé Wolfgang A.
Published: June 2013

Purpose:

To investigate the use of biomathematical models such as tumor control probability (TCP) and normal tissue complication probability (NTCP) as new quality assurance (QA) metrics.

Methods:

Five different types of error (MLC transmission, MLC penumbra, MLC tongue and groove, machine output, and MLC position) were intentionally induced to 40 clinical intensity modulated radiation therapy (IMRT) patient plans (20 H&N cases and 20 prostate cases) to simulate both treatment planning system errors and machine delivery errors in the IMRT QA process. The changes in TCP and NTCP for eight different anatomic structures (H&N: CTV, GTV, both parotids, spinal cord, larynx; prostate: CTV, rectal wall) were calculated as the new QA metrics to quantify the clinical impact on patients. The correlation between the change in TCP/NTCP and the change in selected DVH values was also evaluated. The relation between TCP/NTCP change and the characteristics of the TCP/NTCP curves is discussed.

Results:

ΔTCP and ΔNTCP were summarized for each type of induced error and each structure. The changes/degradations in TCP and NTCP caused by the errors vary widely depending on dose patterns unique to each plan, and are good indicators of each plan's “robustness” to that type of error.

Conclusions:

In thisin silico QA study the authors have demonstrated the possibility of using biomathematical models not only as patient‐specific QA metrics but also as objective indicators that quantify, pretreatment, a plan's robustness with respect to possible error types.
Bacterial Tethering Analysis Reveals a “Run-Reverse-Turn” Mechanism for Pseudomonas Species Motility
Authors: Qian Chen , Wong Chui Ching , Swarup Sanjay , Chiam Keng-Hwee
Published: June 2013

We have developed a program that can accurately analyze the dynamic properties of tethered bacterial cells. The program works especially well with cells that tend to give rise to unstable rotations, such as polar-flagellated bacteria. The program has two novel components. The first dynamically adjusts the center of the cell's rotational trajectories. The second applies piecewise linear approximation to the accumulated rotation curve to reduce noise and separate the motion of bacteria into phases. Thus, it can separate counterclockwise (CCW) and clockwise (CW) rotations distinctly and measure rotational speed accurately. Using this program, we analyzed the properties of tethered
Pseudomonas aeruginosa
and
Pseudomonas putida
cells for the first time. We found that the
Pseudomonas
flagellar motor spends equal time in both CCW and CW phases and that it rotates with the same speed in both phases. In addition, we discovered that the cell body can remain stationary for short periods of time, leading to the existence of a third phase of the flagellar motor which we call “pause.” In addition,
P. aeruginosa
cells adopt longer run lengths, fewer pause frequencies, and shorter pause durations as part of their chemotactic response. We propose that one purpose of the pause phase is to allow the cells to turn at a large angle, where we show that pause durations in free-swimming cells positively correlate with turn angle sizes. Taken together, our results suggest a new “run-reverse-turn” paradigm for polar-flagellated
Pseudomonas
motility that is different from the “run-and-tumble” paradigm established for peritrichous
Escherichia coli
.
Engineering the
meso
-Diaminopimelate Dehydrogenase from Symbiobacterium thermophilum by Site Saturation Mutagenesis for
d
-Phenylalanine Synthesis
Authors: Gao Xiuzhen , Huang Fang , Feng Jinhui , Chen Xi , Zhang Hailing , Wang Zhixiang , Wu Qiaqing , Zhu Dunming
Published: June 2013

In order to enlarge the substrate binding pocket of the
meso
-diaminopimelate dehydrogenase from
Symbiobacterium thermophilum
to accommodate larger 2-keto acids, four amino acid residues (Phe146, Thr171, Arg181, and His227) were targeted for site saturation mutagenesis. Among all mutants, the single mutant H227V had a specific activity of 2.39 ± 0.06 U · mg
−1
, which was 35.1-fold enhancement over the wild-type enzyme.
Improved Bacterial Mutagenesis by High-Frequency Allele Exchange, Demonstrated in Clostridium difficile and Streptococcus suis
Authors: Faulds-Pain Alexandra , Wren Brendan W.
Published: June 2013

Here we show that the frequency of mutant isolation by two-step allele exchange can be improved by increasing the length of homologous DNA and the opportunity for recombination, obviating the need for counterselection markers. These principles are demonstrated in
Clostridium difficile
and
Streptococcus suis
but are likely to be generally applicable.
MtvR Is a Global Small Noncoding Regulatory RNA in Burkholderia cenocepacia
Authors: Ramos Christian G. , Grilo André M. , da Costa Paulo J. P. , Feliciano Joana R. , Leitão Jorge H.
Published: June 2013

Burkholderia cenocepacia
J2315 is a highly epidemic and transmissible clinical isolate of the
Burkholderia cepacia
complex (Bcc), a group of bacteria causing life-threatening respiratory infections among cystic fibrosis patients. This work describes the functional analysis of the 136-nucleotide (nt)-long MtvR small noncoding RNA (sRNA) from the Bcc member
B. cenocepacia
J2315, with homologues restricted to the genus
Burkholderia
. Bioinformatic target predictions revealed a total of 309 mRNAs to be putative MtvR targets. The mRNA levels corresponding to 17 of 19 selected genes were found to be affected when MtvR was either overexpressed or silenced. Analysis of the interaction between MtvR and the
hfq
mRNA, one of its targets, showed that the sRNA binds exclusively to the 5′ untranslated region (UTR) of the
hfq
mRNA. This interaction resulted in decreased protein synthesis, suggesting a negative regulatory effect of MtvR on the RNA chaperone Hfq. Bacterial strains with MtvR silenced or overexpressed exhibited pleiotropic phenotypes related to growth and survival after several stresses, swimming and swarming motilities, biofilm formation, resistance to antibiotics, and ability to colonize and kill the nematode
Caenorhabditis elegans
. Together, the results indicate that the MtvR sRNA is a major posttranscriptional regulator in
B. cenocepacia
.
Allelic Variation in a Simple Sequence Repeat Element of Neisserial
pglB2
and Its Consequences for Protein Expression and Protein Glycosylation
Authors: Viburiene Raimonda , Vik Åshild , Koomey Michael , Børud Bente
Published: June 2013

Neisseria
species express an
O
-linked glycosylation system in which functionally distinct proteins are elaborated with variable glycans. A major source of glycan diversity in
N. meningitidis
results from two distinct
pglB
alleles responsible for the synthesis of either
N
,
N
′-diacetylbacillosamine or glyceramido-acetamido trideoxyhexose that occupy the reducing end of the oligosaccharides. Alternative modifications at C-4 of the precursor UDP-4-amino are attributable to distinct C-terminal domains that dictate either acetyltransferase or glyceramidotransferase activity, encoded by
pglB
and
pglB2
, respectively. Naturally occurring alleles of
pglB2
have homopolymeric tracts of either 7 or 8 adenosines (As) bridging the C-terminal open reading frame (ORF) and the ORF encompassing the conserved N-terminal domain associated with phosphoglycosyltransferase activity. In the work presented here, we explored the consequences of such
pglB2
allele variation and found that, although both alleles are functional vis-à-vis glycosylation, the 7A form results in the expression of a single, multidomain protein, while the 8A variant elicits two single-domain proteins. We also found that the glyceramidotransferase activity-encoding domain is essential to protein glycosylation, showing the critical role of the C-4 modification of the precursor UDP-4-amino in the pathway. These findings were further extended and confirmed by examining the phenotypic consequences of extended poly(A) tract length variation. Although ORFs related to those of
pglB2
are broadly distributed in eubacteria, they are primarily found as two distinct, juxtaposed ORFs. Thus, the neisserial
pglB2
system provides novel insights into the potential influence of hypermutability on modular evolution of proteins by providing a unique snapshot of the progression of ongoing gene fusion.
Brucella BioR Regulator Defines a Complex Regulatory Mechanism for Bacterial Biotin Metabolism
Authors: Feng Youjun , Xu Jie , Zhang Huimin , Chen Zeliang , Srinivas Swaminath
Published: June 2013

The enzyme cofactor biotin (vitamin H or B7) is an energetically expensive molecule whose
de novo
biosynthesis requires 20 ATP equivalents. It seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. Unlike the model regulator BirA, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, BioR has been recently reported by us as an alternative machinery and a new type of GntR family transcriptional factor that can repress the expression of the
bioBFDAZ
operon in the plant pathogen
Agrobacterium tumefaciens
. However, quite unusually, a closely related human pathogen,
Brucella melitensis
, has four putative BioR-binding sites (both
bioR
and
bioY
possess one site in the promoter region, whereas the
bioBFDAZ
[
bio
] operon contains two tandem BioR boxes). This raised the question of whether BioR mediates the complex regulatory network of biotin metabolism. Here, we report that this is the case. The
B. melitensis
BioR ortholog was overexpressed and purified to homogeneity, and its solution structure was found to be dimeric. Functional complementation in a
bioR
isogenic mutant of
A. tumefaciens
elucidated that
Brucella
BioR is a functional repressor. Electrophoretic mobility shift assays demonstrated that the four predicted BioR sites of
Brucella
plus the BioR site of
A. tumefaciens
can all interact with the
Brucella
BioR protein. In a reporter strain that we developed on the basis of a double mutant of
A. tumefaciens
(the Δ
bioR
Δ
bioBFDA
mutant), the β-galactosidase (β-Gal) activity of three plasmid-borne transcriptional fusions (
bioB
bme
-lacZ
,
bioY
bme
-lacZ
, and
bioR
bme
-lacZ
) was dramatically decreased upon overexpression of
Brucella bioR
. Real-time quantitative PCR analyses showed that the expression of
bioBFDA
and
bioY
is significantly elevated upon removal of
bioR
from
B. melitensis
. Together, we conclude that
Brucella
BioR is not only a negative autoregulator but also a repressor of expression of
bioY
and
bio
operons that separately function in biotin transport and the biosynthesis pathway.
Implication of the VirD4 Coupling Protein of the Lvh Type 4 Secretion System in Virulence Phenotypes of Legionella pneumophila
Authors: Bandyopadhyay Purnima , Lang Elza A. S. , Rasaputra Komal S. , Steinman Howard M.
Published: June 2013

The genome of the Philadelphia-1 strain ofLegionella pneumophila, the causative organism of Legionnaires' disease, encodes two virulence-associated type 4 secretion systems (T4SSs), the Dot/Icm type 4B (T4BSS) and the Lvh type 4A (T4ASS). Broth stationary-phase cultures of mostdot/icmmutants are defective in entry and evasion of phagosome acidification. However, those virulence defects can be reversed by incubating broth cultures ofdot/icmmutants in water, termed water stress (WS). WS reversal requires thelvhT4ASS locus, suggesting an interaction between the two T4SSs in producingLegionellavirulence phenotypes. In the current work, the loss of WS reversal in adotAΔlvhmutant of strain JR32 was shown to be attributable to loss of thelvh virD4gene, encoding the putative coupling protein of the T4ASS. Transformation of adotAΔlvhmutant withvirD4also reversed entry and phagosome acidification defects in broth cultures. In addition, broth cultures of Δlvhand ΔvirD4mutants, which weredot/icm+, showed 5-fold and >6-fold increases in translocation of the Dot/Icm translocation substrates, proteins RalF and SidD, respectively. These data demonstrate that the Lvh T4ASS functions in both broth stationary-phase cultures conventionally used for infection and cultures exposed to WS treatment. Our studies in adotAΔlvhmutant and in adot/icm+background establish that VirD4 and the Lvh T4ASS contribute to virulence phenotypes and are consistent with independent functioning of Dot/Icm and Lvh T4SSs or functional substitution of the Lvh VirD4 protein for a component(s) of the Dot/Icm T4BSS.
Key Amino Acid Residues Involved in the Transitions of L- to R-Type Protofilaments of the Salmonella Flagellar Filament
Authors: Hayashi Fumio , Tomaru Hidetoshi , Furukawa Eiji , Ikeda Kanae , Fukano Hiroko , Oosawa Kenji
Published: June 2013

The flagellar filament enables bacteria to swim by functioning as a helical propeller. The filament is a supercoiled assembly of a single protein, flagellin, and is formed by 11 protofilaments arranged in a circle. Bacterial swimming and tumbling correlate with changes of the various helical structures, called polymorphic transformation, that are determined by the ratios of two distinct forms of protofilaments, the L and R types. The polymorphic transformation is caused by transition of the protofilament between L and R types. Elucidation of this transition mechanism has been addressed by comparing the atomic structures of L- and R-type straight filaments or using massive molecular dynamic simulation. Here, we found amino acid residues required for the transition of the protofilament using
fliC
-intragenic suppressor analysis. We isolated a number of revertants producing supercoiled filaments from mutants with straight filaments and identified the second-site mutations in all of the revertants. The results suggest that Asp107, Gly426, and Ser448 and Ser106, Ala416, Ala427, and Arg431 are the key residues involved in inducing supercoiled filaments from the R- and the L-type straight filaments, respectively. Considering the structures of the R- and L-type protofilaments and the relationship between the rotation of the flagellar motor and the polymorphic transformation, we propose that Gly426, Ala427, and Arg431 contribute to the first stage of the transition and that Ser106, Asp107, and Ala416 play a role in propagating the transitions along the flagellar filament.
Systemic lupus erythematosus, pregnancy and carcinoma of the tongue
Authors: Unsworth Jeffrey David , Baldwin Andrew , Byrd Louise
Published: June 2013

We present a case which describes a 29-year-old woman with systemic lupus erythematosus who was treated aggressively with cytotoxic immunosuppression. Five years later and approximately 12 weeks pregnant, she is confirmed as having carcinoma of the tongue. Not wishing to consider termination of her pregnancy, she underwent surgical resection, which included partial glossectomy with microvascular reconstruction. Good oral function (speech and swallowing) was restored within 2 weeks. The pregnancy proceeded relatively uneventfully to 37 weeks gestation when proteinuric hypertension necessitated induction of labour. She remains well with no evidence of recurrence. This case highlights the options available in the treatment of carcinoma of the tongue during pregnancy together with the ethical considerations required, balanced against optimising maternal outcomes.
Small bowel obstruction secondary to a liberated Meckel's enterolith
Authors: Demetriou Vias , McKean David , Briggs James , Moore Niall
Published: June 2013

A 30-year-old woman presented with a short history of abdominal pain which rapidly progressed to absolute constipation. An abdominal radiograph demonstrated a paucity of bowel gas and a 4 cm lesion with concentric laminar calcification projected over the pelvis. A CT scan revealed a 4 cm giant Meckel's diverticulum, downstream of which a laminated mass was impacted in the lumen of the distal ileum causing small bowel obstruction. Subsequent surgery confirmed small bowel obstruction secondary to impaction of a liberated enterolith from the giant Meckel's diverticulum. The history, imaging appearances and surgical findings in this case are classical of this unusual but treatable condition.
Renal calculi in pregnancy? The role of ultralow-dose CT
Authors: Nash Zachary , Mascarenhas Lawrence
Published: June 2013

Presented is a case of an acute, right flank, loin to groin pain in the third trimester of an otherwise uncomplicated pregnancy. Renal calculi was suspected clinically and supported by radiological evidence. Temporising treatment was undertaken successfully by retrograde ureteric stenting, which became blocked, secondarily resulting in a percutaneous nephrostomy. Good symptomatic control was achieved before the delivery at 38 weeks and 1 day gestation. Postpartum intravenous urogram and ureteroscopy did not reveal evidence of calculi. The patient does not recall passing a stone. With existing diagnostic modalities having poor sensitivity and specificity, the clinical role of ultralow-dose CT is explored, in light of recent new evidence.
Nitrofurantoin related pulmonary disease: a clinical reminder
Authors: Reynolds Timothy David , Thomas Jose
Published: June 2013

A 57-year-old woman presented to the admissions unit with a 2-month history of malaise, chest tightness and non-productive cough. An outpatient chest radiograph arranged by her general practitioner was reported as showing ‘changes in keeping with a severe chest infection’ and she had been started on oral antibiotics but her clinical condition subsequently deteriorated. On admission she was febrile (39.2°C) and her oxygen saturation was 99% on 60% oxygen via facemask (rapidly desaturating when supplementary oxygen was removed). Auscultation revealed fine mid-late inspiratory crackles over both lung bases. It transpired that 4 months prior to the onset of symptoms she had been started on nitrofurantoin for prophylaxis against urinary tract infections. The nitrofurantoin was stopped and she was started on prednisolone. Her fever and oxygen saturation gradually improved and she was discharged home after 11 days in the hospital. Her improvement was sustained on outpatient review 8 months later.
A late recurrence of renal cell carcinoma as pancreatic metastases: a rare disease
Authors: Kapoor Rakesh , Kumar Ritesh , Dey P , Mittal B R
Published: June 2013

A man presented with multifocal pancreatic metastases 9 years after nephrectomy for renal cell carcinoma. He was managed with oral sunitinib. He had favourable response to treatment with excellent compliance.
Guillain-Barré syndrome as a paraneoplastic manifestation of disseminated squamous cell carcinoma
Authors: Navani Vishal , Webster Daniel , Williams Sion K , Agranoff Daniel
Published: June 2013

We describe a 65-year-old woman who developed ascending, symmetrical paraesthesia and weakness. This was on a background of metastatic disseminated squamous cell carcinoma, with a likely recurrent mandibular primary. Serum testing for antiganglioside antibodies was strongly positive. Despite a 5-day course of intravenous immunoglobulin, the patient passed away on day 34 of admission. This is the first case, to our knowledge, of Guillain-Barré syndrome in association with squamous cell carcimoma.
Stable graft function on low-dose steroid monotherapy in spite of donor-specific antibodies in renal transplantation combined with stem cell infusion
Authors: Trivedi Hargovind L , Vanikar Aruna V , Dave Shruti D
Published: June 2013

Transplantation using immunosuppression/induction therapies has controlled acute rejections; however, there is no answer for chronic graft attrition. Donor-specific antibodies (DSA) are believed to cause antibody mediated rejections eventually causing chronic graft loss. Regulatory T cells (T-regs) are believed to protect the graft from immune injury. We report a 53-year-old woman transplanted with her son's kidney using donor-specific transfusion and stem cells (SC) under non-myeloablative conditioning of cyclophosphamide, anti-T and anti-B-cell antibodies and Bortezomib. The patient was on low-dose steroid monotherapy under immune monitoring of DSA and serum creatine. Graft biopsy at 1 and 3.5 years post-transplant was unremarkable in spite of the presence of DSA. Peripheral T-regs (pTregs) at 3.5 years post-transplant were 3.54%. This case shows that DSA are not necessarily detrimental to the renal allograft. We further hypothesise that pTregs were induced from SC and sustained to protect this graft from cytotoxic T cells and DSA.
A case of putty kidney without pulmonary tuberculosis
Authors: Nishant Kumar , Sharma Barun Kumar , Philipraj S Joseph , Singh Varun Kumar
Published: June 2013

A 30-year-old woman presented with a 1-year history of a dull ache in her left flank along with recent onset of hypertension. There was no history suggestive of tuberculosis and examination was unremarkable. X-ray showed dense opacity in left renal area. Contrast-enhanced CT revealed a non-enhancing and non-excretory left kidney suggesting autonephrectomy. When a 6 week course of antituberculous therapy (ATT) failed to alleviate her symptoms, surgical nephroureterectomy was performed which resulted in complete resolution of symptoms and well-controlled blood pressure without any medication.
Occupational homicide of law enforcement officers in the US, 1996–2010
Authors: Swedler David I , Kercher Cassandra , Simmons Molly M , Pollack Keshia M
Published: June 2013

Objective

To understand the circumstances surrounding the occupational homicides of law enforcement officers (LEOs) in the USA.

Methods

Narrative text analysis of Federal Bureau of InvestigationLaw Enforcement Officers Killed and Assaultedreports.

Results

A total of 796 officers were killed in the line of duty between 1996 and 2010. The occupational homicide rate during the time peaked in 2001 at 3.76/100 000 (excluding those killed during the September 11 2001 terrorist attacks), and was lowest in 2008 at 1.92/100 000. Most LEOs (67%) were killed by short-barrel firearms; 10% were killed with their own service weapon. The most frequent encounter with a suspect prior to a homicide was responding to a disturbance call.

Conclusions

These results should inform officer training and the policies, as well as procedures used when interacting with suspects, especially when firearms are involved.
Transformation of Visual Signals by Inhibitory Interneurons in Retinal Circuits
Authors: Jadzinsky Pablo D. , Baccus Stephen A.
Published: June 2013

One of the largest mysteries of the brain lies in understanding how higher-level computations are implemented by lower-level operations in neurons and synapses. In particular, in many brain regions inhibitory interneurons represent a diverse class of cells, the individual functional roles of which are unknown. We discuss here how the operations of inhibitory interneurons influence the behavior of a circuit, focusing on recent results in the vertebrate retina. A key role in this understanding is played by a common representation of the visual stimulus that can be applied at different stages. By considering how this stimulus representation changes at each location in the circuit, we can understand how neuron-level operations such as thresholds and inhibition yield circuit-level computations such as how stimulus selectivity and gain are controlled by local and peripheral visual stimuli.
Electrical Compartmentalization in Dendritic Spines
Authors: Yuste Rafael
Published: June 2013

Most excitatory inputs in the CNS contact dendritic spines, avoiding dendritic shafts, so spines must play a key role for neurons. Recent data suggest that, in addition to enhancing connectivity and isolating synaptic biochemistry, spines can behave as electrical compartments independent from their parent dendrites. It is becoming clear that, although spines experience voltages similar to those of dendrites during action potentials (APs), spines must sustain higher depolarizations than do dendritic shafts during excitatory postsynaptic potentials (EPSPs). Synaptic potentials are likely amplified at the spine head and then reduced as they invade the dendrite through the spine neck. These electrical changes, probably due to a combination of passive and active mechanisms, may prevent the saturation of dendrites by the joint activation of many inputs, influence dendritic integration, and contribute to rapid synaptic plasticity. The electrical properties of spines could enable neural circuits to harness a high connectivity, implementing a “synaptic democracy,” where each input can be individually integrated, tallied, and modified in order to generate emergent functional states.
Neuronal Computations in the Olfactory System of Zebrafish
Authors: Friedrich Rainer W.
Published: June 2013

The main olfactory system encodes information about molecules in a combinatorial fashion by distributed spatiotemporal activity patterns. As activity propagates from sensory neurons to the olfactory bulb and to higher brain areas, odor information is processed by multiple transformations of these activity patterns. This review discusses neuronal computations associated with such transformations in the olfactory system of zebrafish, a small vertebrate that offers advantages for the quantitative analysis and manipulation of neuronal activity in the intact brain. The review focuses on pattern decorrelation in the olfactory bulb and on the readout of multiplexed sensory representations in the telencephalic area Dp, the homolog of the olfactory cortex. These computations are difficult to study in larger species and may provide insights into general information-processing strategies in the brain.
Cortical Control of Arm Movements: A Dynamical Systems Perspective
Authors: Shenoy Krishna V. , Sahani Maneesh , Churchland Mark M.
Published: June 2013

Our ability to move is central to everyday life. Investigating the neural control of movement in general, and the cortical control of volitional arm movements in particular, has been a major research focus in recent decades. Studies have involved primarily either attempts to account for single-neuron responses in terms of tuning for movement parameters or attempts to decode movement parameters from populations of tuned neurons. Even though this focus on encoding and decoding has led to many seminal advances, it has not produced an agreed-upon conceptual framework. Interest in understanding the underlying neural dynamics has recently increased, leading to questions such as how does the current population response determine the future population response, and to what purpose? We review how a dynamical systems perspective may help us understand why neural activity evolves the way it does, how neural activity relates to movement parameters, and how a unified conceptual framework may result.
Recent Results in Bottomonium
Authors: Patrignani C. , Pedlar T.K. , Rosner J.L.
Published: June 2013

Great strides have been made in the understanding of bound states of the bottom quark, b, and its antiquark, [Formula: see text], since the discovery of the first Ψ resonances in 1977. These bound states, known as bottomonium, have a rich spectrum whose masses and transition amplitudes shed valuable light on the strong interactions. We review some recent developments in bottomonium physics, including the discovery of the spin-singlet states [Formula: see text] and [Formula: see text], the first D-wave states, one or more candidates for spin-triplet [Formula: see text] excitations, and above-threshold states with strong transitions to states below threshold. We also present information about transitions, production, and signatures of new physics.
The Role of Prophage in Plant-Pathogenic Bacteria
Authors: Varani Alessandro M. , Monteiro-Vitorello Claudia Barros , Nakaya Helder I. , Van Sluys Marie-Anne
Published: June 2013

A diverse set of phage lineages is associated with the bacterial plant-pathogen genomes sequenced to date. Analysis of 37 genomes revealed 5,169 potential genes (approximately 4.3 Mbp) of phage origin, and at least 50% had no function assigned or are nonessential to phage biology. Some phytopathogens have transcriptionally active prophage genes under conditions that mimic plant infection, suggesting an association between plant disease and prophage transcriptional modulation. The role of prophages within genomes for cell biology varies. For pathogens such as Pectobacterium, Pseudomonas, Ralstonia, and Streptomyces, involvement of prophage in disease symptoms has been demonstrated. In Xylella and Xanthomonas, prophage activity is associated with genome rearrangements and strain differentiation. For other pathogens, prophage roles are yet to be established. This review integrates available information in a unique interface ( http://propnav.esalq.usp.br ) that may be assessed to improve research in prophage biology and its association with genome evolution and pathogenicity.
Considerations of Scale in the Analysis of Spatial Pattern of Plant Disease Epidemics
Authors: Turechek William W. , McRoberts Neil
Published: June 2013

Scale is an important but somewhat neglected subject in plant pathology. Scale serves as an abstract concept, providing a framework for organizing observations and theoretical models, and plays a functional role in the organization of ecological communities and physical processes. Rich methodological resources are available to plant pathologists interested in considering either or both aspects of scale in their research. We summarize important concepts in both areas of the literature, particularly as they apply to the spatial pattern of plant disease, and highlight some new results that emphasize the importance of scaling on the emergence of different types of probability distribution in empirical observation. We also highlight the important links between heterogeneity and scale, which are of central importance in plant disease epidemiology and the analysis of spatial pattern. We consider statistical approaches that are available, where actual physical scale is known, and for more conceptual research on hierarchies, where scale plays a more abstract role, particularly for field-based research. For the latter, we highlight methods that plant pathologists could consider to account for the effect of scale in the design of field studies.
Engineering Plant Disease Resistance Based on TAL Effectors
Authors: Schornack Sebastian , Moscou Matthew J. , Ward Eric R. , Horvath Diana M.
Published: June 2013

Transcription activator-like (TAL) effectors are encoded by plant-pathogenic bacteria and induce expression of plant host genes. TAL effectors bind DNA on the basis of a unique code that specifies binding of amino acid residues in repeat units to particular DNA bases in a one-to-one correspondence. This code can be used to predict binding sites of natural TAL effectors and to design novel synthetic DNA-binding domains for targeted genome manipulation. Natural mechanisms of resistance in plants against TAL effector–containing pathogens have given insights into new strategies for disease control.
Religion, Nationalism, and Violence: An Integrated Approach
Authors: Gorski Philip S. , Türkmen-Dervişoğlu Gülay
Published: June 2013

Scholarly work on the nexus of religion, nationalism, and violence is currently fragmented along disciplinary and theoretical lines. In sociology, history, and anthropology, a macro-culturalist approach reigns; in political science, economics, and international relations, a micro-rationalist approach is dominant. Recent attempts at a synthesis ignore religion or fold it into ethnicity. A coherent synthesis capable of adequately accounting for religious-nationalist violence must not only integrate micro and macro, cultural and strategic approaches; it must also include a meso level of elite conflict and boundary maintenance and treat the religious field as potentially autonomous from the cultural field.
Development of concept-based physiology lessons for biomedical engineering undergraduate students
Authors: Nelson Regina K. , Chesler Naomi C. , Strang Kevin T.
Published: June 2013

Physiology is a core requirement in the undergraduate biomedical engineering curriculum. In one or two introductory physiology courses, engineering students must learn physiology sufficiently to support learning in their subsequent engineering courses and careers. As preparation for future learning, physiology instruction centered on concepts may help engineering students to further develop their physiology and biomedical engineering knowledge. Following the Backward Design instructional model, a series of seven concept-based lessons was developed for undergraduate engineering students. These online lessons were created as prerequisite physiology training to prepare students to engage in a collaborative engineering challenge activity. This work is presented as an example of how to convert standard, organ system-based physiology content into concept-based content lessons.
Rationale and resources for teaching the mathematical modeling of athletic training and performance
Authors: Clarke David C. , Skiba Philip F.
Published: June 2013

A number of professions rely on exercise prescription to improve health or athletic performance, including coaching, fitness/personal training, rehabilitation, and exercise physiology. It is therefore advisable that the professionals involved learn the various tools available for designing effective training programs. Mathematical modeling of athletic training and performance, which we henceforth call “performance modeling,” is one such tool. Two models, the critical power (CP) model and the Banister impulse-response (IR) model, offer complementary information. The CP model describes the relationship between work rates and the durations for which an individual can sustain them during constant-work-rate or intermittent exercise. The IR model describes the dynamics by which an individual's performance capacity changes over time as a function of training. Both models elegantly abstract the underlying physiology, and both can accurately fit performance data, such that educating exercise practitioners in the science of performance modeling offers both pedagogical and practical benefits. In addition, performance modeling offers an avenue for introducing mathematical modeling skills to exercise physiology researchers. A principal limitation to the adoption of performance modeling is a lack of education. The goal of this report is therefore to encourage educators of exercise physiology practitioners and researchers to incorporate the science of performance modeling in their curricula and to serve as a resource to support this effort. The resources include a comprehensive review of the concepts associated with the development and use of the models, software to enable hands-on computer exercises, and strategies for teaching the models to different audiences.
Online feedback assessments in physiology: effects on students' learning experiences and outcomes
Authors: Marden Nicole Y. , Ulman Lesley G. , Wilson Fiona S. , Velan Gary M.
Published: June 2013

Online formative assessments have become increasingly popular; however, formal evidence supporting their educational benefits is limited. This study investigated the impact of online feedback quizzes on the learning experiences and outcomes of undergraduate students enrolled in an introductory physiology course. Four quiz models were tested, which differed in the amount of credit available, the number of attempts permitted, and whether the quizzes were invigilated or unsupervised, timed or untimed, or open or closed book. All quizzes were composed of multiple-choice questions and provided immediate individualized feedback. Summative end-of-course examination marks were analyzed with respect to performance in quizzes and were also compared with examination performance in the year before the quizzes were introduced. Online surveys were conducted to gather students' perceptions regarding the quizzes. The vast majority of students perceived online quizzes as a valuable learning tool. For all quiz models tested, there was a significant relationship between performance in quizzes and end-of-course examination scores. Importantly, students who performed poorly in quizzes were more likely to fail the examination, suggesting that formative online quizzes may be a useful tool to identify students in need of assistance. Of the four quiz models, only one quiz model was associated with a significant increase in mean examination performance. This model had the strongest formative focus, allowing multiple unsupervised and untimed attempts. This study suggests that the format of online formative assessments is critical in achieving the desired impact on student learning. Specifically, such assessments are most effective when they are low stakes.
Forgotten hardware: how to urinate in a spacesuit
Authors: Hollins Hunter
Published: June 2013

On May 5, 1961, astronaut Alan Shepard became the first American to fly in space. Although National Aeronautics and Space Administration (NASA) had discounted the need for him to urinate, Shepard did, in his spacesuit, short circuiting his electronic biosensors. With the development of the pressure suit needed for high-altitude and space flight during the 1950s, technicians had developed the means for urine collection. However, cultural mores, combined with a lack of interagency communication, and the technical difficulties of spaceflight made human waste collection a difficult task. Despite the difficulties, technicians at NASA created a successful urine collection device that John Glenn wore on the first Mercury orbital flight on February 20, 1962. With minor modifications, male astronauts used this system to collect urine until the Space Shuttle program. John Glenn's urine collection device is at the National Air and Space Museum and has been on view to the public since 1976.
HNO/cGMP-dependent antihypertrophic actions of isopropylamine-NONOate in neonatal rat cardiomyocytes: potential therapeutic advantages of HNO over NO˙
Authors: Irvine Jennifer C. , Cao Nga , Gossain Swati , Alexander Amy E. , Love Jane E. , Qin Chengxue , Horowitz John D. , Kemp-Harper Barbara K. , Ritchie Rebecca H.
Published: June 2013

Nitroxyl (HNO) is a redox congener of NO˙. We now directly compare the antihypertrophic efficacy of HNO and NO˙ donors in neonatal rat cardiomyocytes and compare their contributing mechanisms of actions in this setting. Isopropylamine-NONOate (IPA-NO) elicited concentration-dependent inhibition of endothelin-1 (ET1)-induced increases in cardiomyocyte size, with similar suppression of hypertrophic genes. Antihypertrophic IPA-NO actions were significantly attenuated by l-cysteine (HNO scavenger), Rp-8-pCTP-cGMPS (cGMP-dependent protein kinase inhibitor), and 1-H-(1,2,4)-oxodiazolo-quinxaline-1-one [ODQ; to target soluble guanylyl cyclase (sGC)] but were unaffected by carboxy-PTIO (NO˙ scavenger) or CGRP8–37 (calcitonin gene-related peptide antagonist). Furthermore, IPA-NO significantly increased cardiomyocyte cGMP 3.5-fold (an l-cysteine-sensitive effect) and stimulated sGC activity threefold, without detectable NO˙ release. IPA-NO also suppressed ET1-induced cardiomyocyte superoxide generation. The pure NO˙ donor diethylamine-NONOate (DEA-NO) reproduced these IPA-NO actions but was sensitive to carboxy-PTIO rather than l-cysteine. Although IPA-NO stimulation of purified sGC was preserved under pyrogallol oxidant stress (in direct contrast to DEA-NO), cardiomyocyte sGC activity after either donor was attenuated by this stress. Excitingly IPA-NO also exhibited acute antihypertrophic actions in response to pressure overload in the intact heart. Together these data strongly suggest that IPA-NO protection against cardiomyocyte hypertrophy is independent of both NO˙ and CGRP but rather utilizes novel HNO activation of cGMP signaling. Thus HNO acutely limits hypertrophy independently of NO˙, even under conditions of elevated superoxide. Development of longer-acting HNO donors may thus represent an attractive new strategy for the treatment of cardiac hypertrophy, as stand-alone and/or add-on therapy to standard care.
Radiation-Induced Carotid Artery Stenosis in a Patient with Carcinoma of the Oral Floor
Authors: Seto Kahori , Yamagata Kenji , Uchida Fumihiko , Yanagawa Toru , Onizawa Kojiro , Bukawa Hiroki
Published: June 2013

Radiation-induced carotid artery stenosis (RI-CS), a life-threatening condition, can occur after external radiation for head and neck cancer. We here describe a case of asymptomatic RI-CS in a 73-year-old patient treated with chemoradiotherapy and radical neck dissection for a basaloid squamous cell carcinoma of the oral floor. Stenosis of the left carotid artery, diagnosed as RI-CS, showed on an MRI performed 1.5 years after radiotherapy. Blood from the left side of the anterior cerebral artery and the middle anterior artery was flowing to the brain through the anterior and posterior communicating arteries, so no stent surgery or other treatment was necessary. The cancer has not recurred during approximately 5 years of followup after radiotherapy, and the patient has had no adverse effects from the RI-CS since it was diagnosed 3.5 years ago. This case emphasizes the necessity of early scrutiny for RI-CS in patients given radiotherapy for oral cancer.